Class: BioInterchange::SO

Inherits:

Object

• Object
• BioInterchange::SO

Defined in:

lib/biointerchange/so.rb

Class Method Summary

• .a_2KB_upstream_variant ⇒ Object

  A sequence variant located within 2KB 5' of a gene.

• .a_3_prime_UTR_variant ⇒ Object

  A UTR variant of the 3' UTR.

• .a_3D_polypeptide_structure_variant ⇒ Object

  A sequence variant that changes the resulting polypeptide structure.

• .a_4_methylcytosine ⇒ Object

  A cytosine methylated at the 4 nitrogen.

• .a_500B_downstream_variant ⇒ Object

  A sequence variant located within a half KB of the end of a gene.

• .a_5_carboxylcytosine ⇒ Object

  A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon.

• .a_5_formylcytosine ⇒ Object

  A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon.

• .a_5_hydroxymethylcytosine ⇒ Object

  A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon.

• .a_5_methylcytosine ⇒ Object

  A cytosine methylated at the 5 carbon.

• .a_5_prime_UTR_premature_start_codon_gain_variant ⇒ Object

  A 5' UTR variant where a premature start codon is gained.

• .a_5_prime_UTR_premature_start_codon_loss_variant ⇒ Object

  A 5' UTR variant where a premature start codon is lost.

• .a_5_prime_UTR_premature_start_codon_variant ⇒ Object

  A 5' UTR variant where a premature start codon is introduced, moved or lost.

• .a_5_prime_UTR_variant ⇒ Object

  A UTR variant of the 5' UTR.

• .a_5KB_downstream_variant ⇒ Object

  A sequence variant located within 5 KB of the end of a gene.

• .a_5KB_upstream_variant ⇒ Object

  A sequence variant located within 5KB 5' of a gene.

• .a_8_oxoadenine ⇒ Object

  A modified DNA adenine base,at the 8 carbon, often the product of DNA damage.

• .a_8_oxoguanine ⇒ Object

  A modified DNA guanine base,at the 8 carbon, often the product of DNA damage.

• .A_box ⇒ Object

  A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG.

• .A_box_type_1 ⇒ Object

  An A box within an RNA polymerase III type 1 promoter.

• .A_box_type_2 ⇒ Object

  An A box within an RNA polymerase III type 2 promoter.

• .A_minor_RNA_motif ⇒ Object

  A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix.

• .A_to_C_transversion ⇒ Object

  A transversion from adenine to cytidine.

• .A_to_G_transition ⇒ Object

  A transition of an adenine to a guanine.

• .A_to_T_transversion ⇒ Object

  A transversion from adenine to thymine.

• .AACCCT_box ⇒ Object

  A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site.

• .aberrant_processed_transcript ⇒ Object

  A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons.

• .Ace2_UAS ⇒ Object

  A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2.

• .active_peptide ⇒ Object

  Active peptides are proteins which are biologically active, released from a precursor molecule.

• .adaptive_island ⇒ Object

  An adaptive island is a genomic island that provides an adaptive advantage to the host.

• .adjacent_to ⇒ Object

  A geometric operator, specified in Egenhofer 1989.

• .AFLP_fragment ⇒ Object

  A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments.

• .alanine ⇒ Object

  A place holder for a cross product with chebi.

• .alanine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding alanyl tRNA.

• .alanyl_tRNA ⇒ Object

  A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.

• .allele ⇒ Object

  An allele is one of a set of coexisting sequence variants of a gene.

• .allelically_excluded ⇒ Object

  Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell.

• .allelically_excluded_gene ⇒ Object

  A gene that is allelically_excluded.

• .allopolyploid ⇒ Object

  A polyploid where the multiple chromosome set was derived from a different organism.

• .alpha_beta_motif ⇒ Object

  A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative.

• .alpha_helix ⇒ Object

  The helix has 3.6 residues per turn which corersponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis.

• .alteration_attribute ⇒ Object

  -- No comment or description provided.

• .alternate_sequence_site ⇒ Object

  Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.

• .alternately_spliced_gene_encodeing_one_transcript ⇒ Object

  -- No comment or description provided.

• .alternately_spliced_gene_encoding_greater_than_one_transcript ⇒ Object

  -- No comment or description provided.

• .alternatively_spliced ⇒ Object

  An attribute describing a situation where a gene may encode for more than 1 transcript.

• .alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping ⇒ Object

  -- No comment or description provided.

• .alternatively_spliced_transcript ⇒ Object

  A transcript that is alternatively spliced.

• .alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping ⇒ Object

  -- No comment or description provided.

• .ambisense_ssRNA_viral_sequence ⇒ Object

  A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity.

• .amino_acid ⇒ Object

  A sequence feature that corresponds to a single amino acid residue in a polypeptide.

• .amino_acid_deletion ⇒ Object

  A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide.

• .amino_acid_insertion ⇒ Object

  A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide.

• .amino_acid_substitution ⇒ Object

  A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide.

• .amplification_origin ⇒ Object

  An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence.

• .anchor_binding_site ⇒ Object

  Part of an edited transcript only.

• .anchor_region ⇒ Object

  A region of a guide_RNA that base-pairs to a target mRNA.

• .androgen_response_element ⇒ Object

  A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen.

• .aneuploid ⇒ Object

  A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number.

• .aneuploid_chromosome ⇒ Object

  A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking.

• .annotation_directed_improved_draft ⇒ Object

  The status of a whole genome sequence,where annotation, and verification of coding regions has occurred.

• .anti_ARRET ⇒ Object

  A non-coding RNA transcript, derived from the transcription of the telomere.

• .anticodon ⇒ Object

  A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.

• .anticodon_loop ⇒ Object

  A sequence of seven nucleotide bases in tRNA which contains the anticodon.

• .antiparallel_beta_strand ⇒ Object

  A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal).

• .antisense ⇒ Object

  A region sequence that is complementary to a sequence of messenger RNA.

• .antisense_lncRNA ⇒ Object

  Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA.

• .antisense_primary_transcript ⇒ Object

  The reverse complement of the primary transcript.

• .antisense_RNA ⇒ Object

  Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA.

• .AP_1_binding_site ⇒ Object

  A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors.

• .apicoplast_chromosome ⇒ Object

  A chromosome originating in an apicoplast.

• .apicoplast_gene ⇒ Object

  A gene from apicoplast sequence.

• .apicoplast_sequence ⇒ Object

  -- No comment or description provided.

• .aptamer ⇒ Object

  DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules.

• .archaeal_intron ⇒ Object

  An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease.

• .archaeosine ⇒ Object

  Archaeosine is a modified 7-deazoguanosine.

• .arginine ⇒ Object

  A place holder for a cross product with chebi.

• .arginine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding arginyl tRNA (SO:0000255).

• .arginyl_tRNA ⇒ Object

  A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.

• .ARIA ⇒ Object

  A non-coding RNA transcript, derived from the transcription of the telomere.

• .ARRET ⇒ Object

  A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats.

• .ARS ⇒ Object

  A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.

• .ARS_consensus_sequence ⇒ Object

  The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC).

• .asparagine ⇒ Object

  A place holder for a cross product with chebi.

• .asparagine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding asparaginyl tRNA (SO:0000256).

• .asparaginyl_tRNA ⇒ Object

  A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.

• .aspartic_acid ⇒ Object

  A place holder for a cross product with chebi.

• .aspartic_acid_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding aspartyl tRNA (SO:0000257).

• .aspartyl_tRNA ⇒ Object

  A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region.

• .ASPE_primer ⇒ Object

  "A primer containing an SNV at the 3' end for accurate genotyping.

• .assembly ⇒ Object

  A region of the genome of known length that is composed by ordering and aligning two or more different regions.

• .assembly_component ⇒ Object

  A region of known length which may be used to manufacture a longer region.

• .assembly_error_correction ⇒ Object

  A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake.

• .associated_with ⇒ Object

  This relationship is vague and up for discussion.

• .assortment_derived_aneuploid ⇒ Object

  Either: -- No comment or description provided.

• .assortment_derived_deficiency ⇒ Object

  Either: -- No comment or description provided.

• .assortment_derived_deficiency_plus_duplication ⇒ Object

  Either: -- No comment or description provided.

• .assortment_derived_duplication ⇒ Object

  Either: -- No comment or description provided.

• .assortment_derived_variation ⇒ Object

  A chromosome variation derived from an event during meiosis.

• .asx_motif ⇒ Object

  A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).

• .asx_turn ⇒ Object

  A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).

• .asx_turn_left_handed_type_one ⇒ Object

  Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees.

• .asx_turn_left_handed_type_two ⇒ Object

  Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees.

• .asx_turn_right_handed_type_one ⇒ Object

  Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees.

• .asx_turn_right_handed_type_two ⇒ Object

  Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees.

• .asymmetric_RNA_internal_loop ⇒ Object

  An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand.

• .attB_site ⇒ Object

  An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site.

• .attC_site ⇒ Object

  An attC site is a sequence required for the integration of a DNA of an integron.

• .attCtn_site ⇒ Object

  An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon.

• .attenuator ⇒ Object

  A sequence segment located within the five prime end of an mRNA that causes premature termination of translation.

• .attI_site ⇒ Object

  A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place.

• .attL_site ⇒ Object

  A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site.

• .attP_site ⇒ Object

  An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome.

• .attR_site ⇒ Object

  A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site.

• .AU_rich_element ⇒ Object

  A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers.

• .autocatalytically_spliced_intron ⇒ Object

  A self spliced intron.

• .autopolyploid ⇒ Object

  A polyploid where the multiple chromosome set was derived from the same organism.

• .autoregulated ⇒ Object

  The gene product is involved in its own transcriptional regulation.

• .autosynaptic_chromosome ⇒ Object

  An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome.

• .B_box ⇒ Object

  A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC.

• .BAC ⇒ Object

  Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host.

• .BAC_clone ⇒ Object

  -- No comment or description provided.

• .BAC_cloned_genomic_insert ⇒ Object

  Requested by Andy Schroder - Flybase Harvard, Nov 2006.

• .BAC_end ⇒ Object

  A region of sequence from the end of a BAC clone that may provide a highly specific marker.

• .BAC_read_contig ⇒ Object

  A contig of BAC reads.

• .bacterial_RNApol_promoter ⇒ Object

  A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.

• .bacterial_RNApol_promoter_region ⇒ Object

  A region which is part of a bacterial RNA polymerase promoter.

• .bacterial_RNApol_promoter_sigma54 ⇒ Object

  -- No comment or description provided.

• .bacterial_RNApol_promoter_sigma_70 ⇒ Object

  -- No comment or description provided.

• .bacterial_RNApol_promoter_sigma_ecf ⇒ Object

  A bacterial promoter with sigma ecf factor binding dependency.

• .bacterial_terminator ⇒ Object

  A terminator signal for bacterial transcription.

• .base ⇒ Object

  A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.

• .base_call_error_correction ⇒ Object

  A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake.

• .base_pair ⇒ Object

  -- No comment or description provided.

• .benign_variant ⇒ Object

  -- No comment or description provided.

• .beta_bulge ⇒ Object

  A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees.

• .beta_bulge_loop ⇒ Object

  A motif of three residues within a beta-sheet consisting of two H-bonds.

• .beta_bulge_loop_five ⇒ Object

  A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3.

• .beta_bulge_loop_six ⇒ Object

  A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4.

• .beta_strand ⇒ Object

  A beta strand describes a single length of polypeptide chain that forms part of a beta sheet.

• .beta_turn ⇒ Object

  A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth.

• .beta_turn_left_handed_type_one ⇒ Object

  Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth.

• .beta_turn_left_handed_type_two ⇒ Object

  Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth.

• .beta_turn_right_handed_type_one ⇒ Object

  Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth.

• .beta_turn_right_handed_type_two ⇒ Object

  Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth.

• .beta_turn_type_eight ⇒ Object

  A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees.

• .beta_turn_type_six ⇒ Object

  A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline.

• .beta_turn_type_six_a ⇒ Object

  A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees.

• .beta_turn_type_six_a_one ⇒ Object

  -- No comment or description provided.

• .beta_turn_type_six_a_two ⇒ Object

  -- No comment or description provided.

• .beta_turn_type_six_b ⇒ Object

  A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees.

• .bidirectional_promoter ⇒ Object

  -- No comment or description provided.

• .binding_site ⇒ Object

  A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules.

• .biochemical_region_of_peptide ⇒ Object

  A region of a peptide that is involved in a biochemical function.

• .biological_region ⇒ Object

  A region defined by its disposition to be involved in a biological process.

• .biomaterial_region ⇒ Object

  A region which is intended for use in an experiment.

• .bipartite_duplication ⇒ Object

  An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break.

• .bipartite_inversion ⇒ Object

  A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed).

• .blocked_reading_frame ⇒ Object

  A reading_frame that is interrupted by one or more stop codons; usually identified through intergenomic sequence comparisons.

• .blunt_end_restriction_enzyme_cleavage_junction ⇒ Object

  A restriction enzyme cleavage site where both strands are cut at the same position.

• .blunt_end_restriction_enzyme_cleavage_site ⇒ Object

  -- No comment or description provided.

• .bound_by_factor ⇒ Object

  An attribute describing a sequence that is bound by another molecule.

• .bound_by_nucleic_acid ⇒ Object

  An attribute describing a sequence that is bound by a nucleic acid.

• .bound_by_protein ⇒ Object

  An attribute describing a sequence that is bound by a protein.

• .branch_site ⇒ Object

  A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing.

• .BREd_motif ⇒ Object

  A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G).

• .BREu_motif ⇒ Object

  A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1).

• .Bruno_response_element ⇒ Object

  A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.

• .C_box ⇒ Object

  An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn.

• .C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene.

• .C_D_box_snoRNA ⇒ Object

  Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA.

• .C_D_box_snoRNA_encoding ⇒ Object

  -- No comment or description provided.

• .C_D_box_snoRNA_primary_transcript ⇒ Object

  A primary transcript encoding a small nucleolar RNA of the box C/D family.

• .C_gene_segment ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205).

• .C_region ⇒ Object

  The constant region of an immunoglobulin polypeptide sequence.

• .c_terminal_region ⇒ Object

  The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa).

• .C_to_A_transversion ⇒ Object

  A transversion from cytidine to adenine.

• .C_to_G_transversion ⇒ Object

  -- No comment or description provided.

• .C_to_T_transition ⇒ Object

  A transition of a cytidine to a thymine.

• .C_to_T_transition_at_pCpG_site ⇒ Object

  The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine.

• .CAAT_signal ⇒ Object

  Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT.

• .CAGE_cluster ⇒ Object

  A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region.

• .CAGE_tag ⇒ Object

  A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites.

• .candidate_gene ⇒ Object

  A gene suspected of being involved in the expression of a trait.

• .canonical_five_prime_splice_site ⇒ Object

  The canonical 5' splice site has the sequence "GT".

• .canonical_splice_site ⇒ Object

  The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively.

• .canonical_three_prime_splice_site ⇒ Object

  The canonical 3' splice site has the sequence "AG".

• .cap ⇒ Object

  A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA.

• .capped ⇒ Object

  An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end.

• .capped_mRNA ⇒ Object

  An mRNA that is capped.

• .capped_primary_transcript ⇒ Object

  A primary transcript that is capped.

• .cassette_array_member ⇒ Object

  -- No comment or description provided.

• .cassette_pseudogene ⇒ Object

  A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy.

• .catalytic_residue ⇒ Object

  Amino acid involved in the activity of an enzyme.

• .catmat_left_handed_four ⇒ Object

  A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170.

• .catmat_left_handed_three ⇒ Object

  A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170.

• .catmat_right_handed_four ⇒ Object

  A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170.

• .catmat_right_handed_three ⇒ Object

  A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170.

• .CCA_tail ⇒ Object

  Base sequence at the 3' end of a tRNA.

• .CCAAT_motif ⇒ Object

  A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels.

• .cDNA ⇒ Object

  DNA synthesized by reverse transcriptase using RNA as a template.

• .cDNA_clone ⇒ Object

  Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host.

• .cDNA_match ⇒ Object

  A match against cDNA sequence.

• .CDRE_motif ⇒ Object

  An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin.

• .CDS ⇒ Object

  A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.

• .CDS_fragment ⇒ Object

  -- No comment or description provided.

• .CDS_independently_known ⇒ Object

  A CDS with the evidence status of being independently known.

• .CDS_predicted ⇒ Object

  A CDS that is predicted.

• .CDS_region ⇒ Object

  A region of a CDS.

• .CDS_supported_by_domain_match_data ⇒ Object

  A CDS that is supported by domain similarity.

• .CDS_supported_by_EST_or_cDNA_data ⇒ Object

  A CDS that is supported by similarity to EST or cDNA data.

• .CDS_supported_by_sequence_similarity_data ⇒ Object

  A CDS that is supported by sequence similarity data.

• .central_hydrophobic_region_of_signal_peptide ⇒ Object

  The central, hydrophobic region of the signal peptide (approx 7-15 aa).

• .centromere ⇒ Object

  A region of chromosome where the spindle fibers attach during mitosis and meiosis.

• .centromere_DNA_Element_I ⇒ Object

  A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p).

• .centromere_DNA_Element_II ⇒ Object

  A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length.

• .centromere_DNA_Element_III ⇒ Object

  A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex.

• .centromeric_repeat ⇒ Object

  A repeat region found within the modular centromere.

• .chimeric_cDNA_clone ⇒ Object

  A cDNA clone invalidated because it is chimeric.

• .ChIP_seq_region ⇒ Object

  A region of sequence identified by CHiP seq technology to contain a protein binding site.

• .chloroplast_chromosome ⇒ Object

  A chromosome originating in a chloroplast.

• .chloroplast_DNA ⇒ Object

  This term is used by MO.

• .chloroplast_DNA_read ⇒ Object

  A sequencer read of a chloroplast DNA sample.

• .chloroplast_sequence ⇒ Object

  -- No comment or description provided.

• .chromoplast_chromosome ⇒ Object

  A chromosome originating in a chromoplast.

• .chromoplast_gene ⇒ Object

  A gene from chromoplast_sequence.

• .chromoplast_sequence ⇒ Object

  -- No comment or description provided.

• .chromosomal_deletion ⇒ Object

  An incomplete chromosome.

• .chromosomal_duplication ⇒ Object

  An extra chromosome.

• .chromosomal_inversion ⇒ Object

  An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type.

• .chromosomal_regulatory_element ⇒ Object

  -- No comment or description provided.

• .chromosomal_structural_element ⇒ Object

  -- No comment or description provided.

• .chromosomal_translocation ⇒ Object

  An interchromosomal mutation.

• .chromosomal_transposition ⇒ Object

  A chromosome structure variant whereby a region of a chromosome has been transferred to another position.

• .chromosomal_variation_attribute ⇒ Object

  -- No comment or description provided.

• .chromosomally_aberrant_genome ⇒ Object

  -- No comment or description provided.

• .chromosome ⇒ Object

  Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.

• .chromosome_arm ⇒ Object

  A region of the chromosome between the centromere and the telomere.

• .chromosome_band ⇒ Object

  A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.

• .chromosome_breakage_sequence ⇒ Object

  A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation.

• .chromosome_breakpoint ⇒ Object

  -- No comment or description provided.

• .chromosome_fission ⇒ Object

  A chromosome that occurred by the division of a larger chromosome.

• .chromosome_number_variation ⇒ Object

  A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number.

• .chromosome_part ⇒ Object

  A region of a chromosome.

• .chromosome_structure_variation ⇒ Object

  -- No comment or description provided.

• .chromosome_variation ⇒ Object

  -- No comment or description provided.

• .circular ⇒ Object

  A quality of a nucleotide polymer that has no terminal nucleotide residues.

• .circular_double_stranded_DNA_chromosome ⇒ Object

  Structural unit composed of a self-replicating, double-stranded, circular DNA molecule.

• .circular_double_stranded_RNA_chromosome ⇒ Object

  Structural unit composed of a self-replicating, double-stranded, circular RNA molecule.

• .circular_single_stranded_DNA_chromosome ⇒ Object

  Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.

• .circular_single_stranded_RNA_chromosome ⇒ Object

  Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.

• .cis_regulatory_frameshift_element ⇒ Object

  A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence.

• .cis_splice_site ⇒ Object

  Intronic 2 bp region bordering exon.

• .class_I_RNA ⇒ Object

  Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure.

• .class_II_RNA ⇒ Object

  Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure.

• .cleaved_for_gpi_anchor_region ⇒ Object

  The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor.

• .cleaved_initiator_methionine ⇒ Object

  The initiator methionine that has been cleaved from a mature polypeptide sequence.

• .cleaved_peptide_region ⇒ Object

  The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation.

• .clip ⇒ Object

  Part of the primary transcript that is clipped off during processing.

• .clone ⇒ Object

  A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism.

• .clone_attribute ⇒ Object

  -- No comment or description provided.

• .clone_end ⇒ Object

  A read from an end of the clone sequence.

• .clone_insert ⇒ Object

  The region of sequence that has been inserted and is being propagated by the clone.

• .clone_insert_end ⇒ Object

  The end of the clone insert.

• .clone_insert_start ⇒ Object

  Either: The start of the clone insert.

• .cloned ⇒ Object

  -- No comment or description provided.

• .cloned_cDNA ⇒ Object

  -- No comment or description provided.

• .cloned_cDNA_insert ⇒ Object

  A clone insert made from cDNA.

• .cloned_genomic ⇒ Object

  -- No comment or description provided.

• .cloned_genomic_insert ⇒ Object

  A clone insert made from genomic DNA.

• .cloned_region ⇒ Object

  Added in response to Lynn Crosby.

• .coding_conserved_region ⇒ Object

  Coding region of sequence similarity by descent from a common ancestor.

• .coding_end ⇒ Object

  The last base to be translated into protein.

• .coding_exon ⇒ Object

  An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).

• .coding_region_of_exon ⇒ Object

  The region of an exon that encodes for protein sequence.

• .coding_sequence_variant ⇒ Object

  A sequence variant that changes the coding sequence.

• .coding_start ⇒ Object

  The first base to be translated into protein.

• .coding_transcript_intron_variant ⇒ Object

  A transcript variant occurring within an intron of a coding transcript.

• .coding_transcript_variant ⇒ Object

  A transcript variant of a protein coding gene.

• .coding_variant_quality ⇒ Object

  -- No comment or description provided.

• .codon ⇒ Object

  A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS.

• .codon_redefined ⇒ Object

  An attribute describing the alteration of codon meaning.

• .coiled_coil ⇒ Object

  A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope.

• .cointegrated_plasmid ⇒ Object

  A MGE region consisting of two fused plasmids resulting from a replicative transposition event.

• .common_variant ⇒ Object

  -- No comment or description provided.

• .compensatory_transcript_secondary_structure_variant ⇒ Object

  A secondary structure variant that compensate for the change made by a previous variant.

• .complete_evidence_for_feature ⇒ Object

  B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.

• .complex_3D_structural_variant ⇒ Object

  A sequence variant that changes the resulting polypeptide structure.

• .complex_change_of_translational_product_variant ⇒ Object

  -- No comment or description provided.

• .complex_chromosomal_mutation ⇒ Object

  A chromosome structure variant with 4 or more breakpoints.

• .complex_structural_alteration ⇒ Object

  A structural sequence alteration or rearrangement encompassing one or more genome fragments.

• .complex_substitution ⇒ Object

  When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used.

• .complex_transcript_variant ⇒ Object

  A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.

• .compositionally_biased_region_of_peptide ⇒ Object

  Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length.

• .compound_chromosome ⇒ Object

  A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms.

• .compound_chromosome_arm ⇒ Object

  FLAG - this term is should probably be a part of rather than an is_a.

• .computed_feature ⇒ Object

  -- No comment or description provided.

• .computed_feature_by_similarity ⇒ Object

  . (http://purl.obolibrary.org/obo/SO_0000311).

• .conformational_change_variant ⇒ Object

  A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence.

• .conformational_switch ⇒ Object

  A region of a polypeptide, involved in the transition from one conformational state to another.

• .conjugative_transposon ⇒ Object

  A transposon that encodes function required for conjugation.

• .connects_on ⇒ Object

  X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z.

• .consensus ⇒ Object

  Term added Dec 06 to comply with mapping to MGED terms.

• .consensus_AFLP_fragment ⇒ Object

  A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input.

• .consensus_gDNA ⇒ Object

  Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input.

• .consensus_mRNA ⇒ Object

  DO not obsolete without considering MGED mapping.

• .consensus_region ⇒ Object

  DO not obsolete without considering MGED mapping.

• .conservative_amino_acid_substitution ⇒ Object

  A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide.

• .conservative_inframe_deletion ⇒ Object

  An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons.

• .conservative_inframe_insertion ⇒ Object

  An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons.

• .conservative_missense_variant ⇒ Object

  A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid.

• .conserved ⇒ Object

  -- No comment or description provided.

• .conserved_region ⇒ Object

  Region of sequence similarity by descent from a common ancestor.

• .contained_by ⇒ Object

  X contained_by Y iff X starts after start of Y and X ends before end of Y.

• .contains ⇒ Object

  The inverse of contained_by.

• .contig ⇒ Object

  A contiguous sequence derived from sequence assembly.

• .contig_collection ⇒ Object

  A collection of contigs.

• .contig_read ⇒ Object

  A DNA sequencer read which is part of a contig.

• .copy_number_change ⇒ Object

  A sequence variant where copies of a feature (CNV) are either increased or decreased.

• .copy_number_decrease ⇒ Object

  A sequence variant where copies of a feature are decreased relative to the reference.

• .copy_number_gain ⇒ Object

  A sequence alteration whereby the copy number of a given regions is greater than the reference sequence.

• .copy_number_increase ⇒ Object

  A sequence variant where copies of a feature are increased relative to the reference.

• .copy_number_loss ⇒ Object

  A sequence alteration whereby the copy number of a given region is less than the reference sequence.

• .copy_number_variation ⇒ Object

  A variation that increases or decreases the copy number of a given region.

• .core_promoter_element ⇒ Object

  -- No comment or description provided.

• .cosmid ⇒ Object

  A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites.

• .cosmid_clone ⇒ Object

  -- No comment or description provided.

• .covalent_binding_site ⇒ Object

  Binding involving a covalent bond.

• .CpG_island ⇒ Object

  Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.

• .CRE ⇒ Object

  A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors.

• .CRISPR ⇒ Object

  Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences.

• .CRM ⇒ Object

  A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities.

• .cross_genome_match ⇒ Object

  A nucleotide match against a sequence from another organism.

• .cross_link ⇒ Object

  Posttranslationally formed amino acid bonds.

• .cryptic ⇒ Object

  A feature_attribute describing a feature that is not manifest under normal conditions.

• .cryptic_gene ⇒ Object

  A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning.

• .cryptic_prophage ⇒ Object

  A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes.

• .cryptic_splice_acceptor ⇒ Object

  A sequence variant whereby a new splice site is created due to the activation of a new acceptor.

• .cryptic_splice_donor ⇒ Object

  A sequence variant whereby a new splice site is created due to the activation of a new donor.

• .cryptic_splice_site ⇒ Object

  A splice site that is in part of the transcript not normally spliced.

• .cryptic_splice_site_variant ⇒ Object

  A sequence variant causing a new (functional) splice site.

• .cryptogene ⇒ Object

  A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence.

• .CSL_response_element ⇒ Object

  A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors.

• .CsrB_RsmB_RNA ⇒ Object

  An enterobacterial RNA that binds the CsrA protein.

• .ct_gene ⇒ Object

  A gene from chloroplast sequence.

• .CTCF_binding_site ⇒ Object

  A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor.

• .CTG_start_codon ⇒ Object

  A non-canonical start codon of sequence CTG.

• .CuRE ⇒ Object

  A promoter element bound by copper ion-sensing transcription factors such as S.

• .cyanelle_chromosome ⇒ Object

  A chromosome originating in a cyanelle.

• .cyanelle_gene ⇒ Object

  A gene from cyanelle sequence.

• .cyanelle_sequence ⇒ Object

  -- No comment or description provided.

• .cyclic_translocation ⇒ Object

  A chromosomal translocation whereby three breaks occurred in three different chromosomes.

• .cysteine ⇒ Object

  A place holder for a cross product with chebi.

• .cysteine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding cysteinyl tRNA (SO:0000258).

• .cysteinyl_tRNA ⇒ Object

  A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region.

• .cytoplasmic_polypeptide_region ⇒ Object

  Polypeptide region that is localized inside the cytoplasm.

• .D_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene.

• .D_DJ_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene.

• .D_DJ_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene.

• .D_DJ_J_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene.

• .D_DJ_J_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene.

• .D_gene_recombination_feature ⇒ Object

  -- No comment or description provided.

• .D_gene_segment ⇒ Object

  Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment.

• .D_J_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene.

• .D_J_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene.

• .D_loop ⇒ Object

  Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein.

• .DArT_marker ⇒ Object

  A genetic marker, discovered using Diversity Arrays Technology (DArT) technology.

• .databank_entry ⇒ Object

  The sequence referred to by an entry in a databank such as Genbank or SwissProt.

• .dCAPS_primer ⇒ Object

  A primer with one or more mis-matches to the DNA template corresponding to a position within a restriction enzyme recognition site.

• .DCE ⇒ Object

  A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS.

• .DCE_SI ⇒ Object

  A sub element of the DCE core promoter element, with consensus sequence CTTC.

• .DCE_SII ⇒ Object

  A sub element of the DCE core promoter element with consensus sequence CTGT.

• .DCE_SIII ⇒ Object

  A sub element of the DCE core promoter element with consensus sequence AGC.

• .DDB_box ⇒ Object

  A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases.

• .de_novo_variant ⇒ Object

  -- No comment or description provided.

• .decayed_exon ⇒ Object

  A non-functional descendant of an exon.

• .decreased_polyadenylation_variant ⇒ Object

  A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference.

• .decreased_transcript_level_variant ⇒ Object

  A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence.

• .decreased_transcript_stability_variant ⇒ Object

  A sequence variant that decreases transcript stability with respect to a reference sequence.

• .decreased_transcription_rate_variant ⇒ Object

  A sequence variant that decreases the rate of transcription with respect to a reference sequence.

• .decreased_translational_product_level ⇒ Object

  A sequence variant which decreases the translational product level with respect to a reference sequence.

• .defective_conjugative_transposon ⇒ Object

  An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation.

• .deficient_interchromosomal_transposition ⇒ Object

  An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining.

• .deficient_intrachromosomal_transposition ⇒ Object

  An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining.

• .deficient_inversion ⇒ Object

  A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted.

• .deficient_translocation ⇒ Object

  A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining.

• .delete ⇒ Object

  To remove a subsection of sequence.

• .delete_U ⇒ Object

  An edit to delete a uridine.

• .deletion ⇒ Object

  The point at which one or more contiguous nucleotides were excised.

• .deletion_breakpoint ⇒ Object

  The point within a chromosome where a deletion begins or ends.

• .deletion_junction ⇒ Object

  The space between two bases in a sequence which marks the position where a deletion has occurred.

• .derives_from ⇒ Object

  -- No comment or description provided.

• .designed_sequence ⇒ Object

  -- No comment or description provided.

• .destruction_box ⇒ Object

  A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C.

• .dexstrosynaptic_chromosome ⇒ Object

  An autosynaptic chromosome carrying the two right (D = dextro) telomeres.

• .dg_repeat ⇒ Object

  A repeat region which is part of the regional centromere outer repeat region.

• .dh_repeat ⇒ Object

  A repeat region which is part of the regional centromere outer repeat region.

• .DHU_loop ⇒ Object

  Non-base-paired sequence of nucleotide bases in tRNA.

• .dicistronic ⇒ Object

  An attribute describing a sequence that contains the code for two gene products.

• .dicistronic_mRNA ⇒ Object

  An mRNA that has the quality dicistronic.

• .dicistronic_primary_transcript ⇒ Object

  A primary transcript that has the quality dicistronic.

• .dicistronic_transcript ⇒ Object

  A transcript that is dicistronic.

• .dif_site ⇒ Object

  A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase.

• .dihydrouridine ⇒ Object

  A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring.

• .dinucleotide_repeat_microsatellite_feature ⇒ Object

  -- No comment or description provided.

• .diplotype ⇒ Object

  A diplotype is a pair of haplotypes from a given individual.

• .direct ⇒ Object

  A quality of an insertion where the insert is not in a cytologically inverted orientation.

• .direct_repeat ⇒ Object

  A repeat where the same sequence is repeated in the same direction.

• .direct_tandem_duplication ⇒ Object

  A tandem duplication where the individual regions are in the same orientation.

• .direction_attribute ⇒ Object

  -- No comment or description provided.

• .disconnected_from ⇒ Object

  X is disconnected_from Y iff it is not the case that X overlaps Y.

• .disease_associated_variant ⇒ Object

  -- No comment or description provided.

• .disease_causing_variant ⇒ Object

  -- No comment or description provided.

• .dispersed_repeat ⇒ Object

  A repeat that is located at dispersed sites in the genome.

• .disruptive_inframe_deletion ⇒ Object

  An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon.

• .disruptive_inframe_insertion ⇒ Object

  An inframe_increase_in_cds_length that inserts one or more codons into the coding sequence within an existing codon.

• .distal_duplication ⇒ Object

  A duplication of the distal region of a chromosome.

• .distal_promoter_element ⇒ Object

  -- No comment or description provided.

• .distant_three_prime_recoding_signal ⇒ Object

  A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon.

• .disulfide_bond ⇒ Object

  The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules.

• .DJ_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene.

• .DJ_gene_segment ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment.

• .DJ_J_C_cluster ⇒ Object

  Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE.

• .DJ_J_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene.

• .DMv1_motif ⇒ Object

  A promoter motif with consensus sequence CARCCCT.

• .DMv2_motif ⇒ Object

  A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS.

• .DMv3_motif ⇒ Object

  A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS.

• .DMv4_motif ⇒ Object

  A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1).

• .DMv5_motif ⇒ Object

  A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS.

• .DNA ⇒ Object

  An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone.

• .DNA_aptamer ⇒ Object

  DNA molecules that have been selected from random pools based on their ability to bind other molecules.

• .DNA_binding_site ⇒ Object

  A binding site that, in the molecule, interacts selectively and non-covalently with DNA.

• .DNA_chromosome ⇒ Object

  Structural unit composed of a self-replicating, DNA molecule.

• .DNA_constraint_sequence ⇒ Object

  A double-stranded DNA used to control macromolecular structure and function.

• .DNA_invertase_target_sequence ⇒ Object

  -- No comment or description provided.

• .DNA_motif ⇒ Object

  A motif that is active in the DNA form of the sequence.

• .DNA_replication_mode ⇒ Object

  This has been obsoleted as it represents a process.

• .DNA_sequence_secondary_structure ⇒ Object

  A folded DNA sequence.

• .DNA_transposon ⇒ Object

  A transposon where the mechanism of transposition is via a DNA intermediate.

• .DNAseI_hypersensitive_site ⇒ Object

  -- No comment or description provided.

• .DNAzyme ⇒ Object

  A DNA sequence with catalytic activity.

• .double ⇒ Object

  Attributes added to describe the different kinds of replicon.

• .double_stranded_cDNA ⇒ Object

  -- No comment or description provided.

• .double_stranded_DNA_chromosome ⇒ Object

  Structural unit composed of a self-replicating, double-stranded DNA molecule.

• .double_stranded_RNA_chromosome ⇒ Object

  Structural unit composed of a self-replicating, double-stranded RNA molecule.

• .downstream_gene_variant ⇒ Object

  A sequence variant located 3' of a gene.

• .downstream_transcript_variant ⇒ Object

  Requested by Graham Ritchie, EBI/Sanger.

• .DPE1_motif ⇒ Object

  A promoter motif with consensus sequence CGGACGT.

• .DPE_motif ⇒ Object

  A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1).

• .DRE ⇒ Object

  A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis.

• .DRE_motif ⇒ Object

  A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS.

• .ds_DNA_viral_sequence ⇒ Object

  A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA.

• .ds_oligo ⇒ Object

  A double stranded oligonucleotide.

• .ds_RNA_viral_sequence ⇒ Object

  A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA.

• .DSR_motif ⇒ Object

  The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC.

• .DsrA_RNA ⇒ Object

  DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS.

• .duplicated_pseudogene ⇒ Object

  A pseudogene that arose via gene duplication.

• .duplication ⇒ Object

  An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome.

• .duplication_attribute ⇒ Object

  -- No comment or description provided.

• .dye_terminator_read ⇒ Object

  A read produced by the dye terminator method of sequencing.

• .E_box_motif ⇒ Object

  A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS.

• .edit_operation ⇒ Object

  -- No comment or description provided.

• .edited ⇒ Object

  An attribute describing a sequence that is modified by editing.

• .edited_by_A_to_I_substitution ⇒ Object

  -- No comment or description provided.

• .edited_by_C_insertion_and_dinucleotide_insertion ⇒ Object

  -- No comment or description provided.

• .edited_by_C_to_U_substitution ⇒ Object

  -- No comment or description provided.

• .edited_by_G_addition ⇒ Object

  -- No comment or description provided.

• .edited_CDS ⇒ Object

  A CDS that is edited.

• .edited_from ⇒ Object

  -- No comment or description provided.

• .edited_mRNA ⇒ Object

  An mRNA that is edited.

• .edited_to ⇒ Object

  -- No comment or description provided.

• .edited_transcript ⇒ Object

  A transcript that is edited.

• .edited_transcript_by_A_to_I_substitution ⇒ Object

  A transcript that has been edited by A to I substitution.

• .edited_transcript_feature ⇒ Object

  A locatable feature on a transcript that is edited.

• .editing_block ⇒ Object

  Edited mRNA sequence mediated by a single guide RNA (SO:0000602).

• .editing_domain ⇒ Object

  Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602).

• .editing_variant ⇒ Object

  A transcript processing variant whereby the process of editing is disrupted with respect to the reference.

• .eight_cutter_restriction_site ⇒ Object

  -- No comment or description provided.

• .elongated_in_frame_polypeptide_C_terminal ⇒ Object

  A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus.

• .elongated_in_frame_polypeptide_N_terminal_elongation ⇒ Object

  A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus.

• .elongated_out_of_frame_polypeptide_C_terminal ⇒ Object

  A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus.

• .elongated_out_of_frame_polypeptide_N_terminal ⇒ Object

  A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus.

• .elongated_polypeptide ⇒ Object

  A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence.

• .elongated_polypeptide_C_terminal ⇒ Object

  A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus.

• .elongated_polypeptide_N_terminal ⇒ Object

  A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus.

• .encodes_1_polypeptide ⇒ Object

  A gene that is alternately spliced, but encodes only one polypeptide.

• .encodes_alternate_transcription_start_sites ⇒ Object

  -- No comment or description provided.

• .encodes_alternately_spliced_transcripts ⇒ Object

  A gene that encodes more than one transcript.

• .encodes_different_polypeptides_different_stop ⇒ Object

  A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons.

• .encodes_disjoint_polypeptides ⇒ Object

  A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences.

• .encodes_greater_than_1_polypeptide ⇒ Object

  A gene that is alternately spliced, and encodes more than one polypeptide.

• .encodes_overlapping_peptides ⇒ Object

  A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences.

• .encodes_overlapping_peptides_different_start ⇒ Object

  A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons.

• .encodes_overlapping_polypeptides_different_start_and_stop ⇒ Object

  A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons.

• .end_overlapping_gene ⇒ Object

  -- No comment or description provided.

• .endogenous_retroviral_gene ⇒ Object

  A proviral gene with origin endogenous retrovirus.

• .endogenous_retroviral_sequence ⇒ Object

  -- No comment or description provided.

• .endonuclease_spliced_intron ⇒ Object

  An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification.

• .endosomal_localization_signal ⇒ Object

  A polypeptide region that targets a polypeptide to the endosome.

• .engineered ⇒ Object

  An attribute to describe a region that was modified in vitro.

• .engineered_DNA ⇒ Object

  -- No comment or description provided.

• .engineered_episome ⇒ Object

  An episome that is engineered.

• .engineered_foreign_gene ⇒ Object

  A gene that is engineered and foreign.

• .engineered_foreign_region ⇒ Object

  A region that is engineered and foreign.

• .engineered_foreign_repetitive_element ⇒ Object

  A repetitive element that is engineered and foreign.

• .engineered_foreign_transposable_element ⇒ Object

  A transposable_element that is engineered and foreign.

• .engineered_foreign_transposable_element_gene ⇒ Object

  A transposable_element that is engineered and foreign.

• .engineered_fusion_gene ⇒ Object

  A fusion gene that is engineered.

• .engineered_gene ⇒ Object

  A gene that is engineered.

• .engineered_insert ⇒ Object

  A clone insert that is engineered.

• .engineered_plasmid ⇒ Object

  A plasmid that is engineered.

• .engineered_region ⇒ Object

  A region that is engineered.

• .engineered_rescue_region ⇒ Object

  A rescue region that is engineered.

• .engineered_tag ⇒ Object

  A tag that is engineered.

• .engineered_transposable_element ⇒ Object

  TE that has been modified by manipulations in vitro.

• .enhanceosome ⇒ Object

  -- No comment or description provided.

• .enhancer ⇒ Object

  A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.

• .enhancer_attribute ⇒ Object

  -- No comment or description provided.

• .enhancer_binding_site ⇒ Object

  A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.

• .enhancer_bound_by_factor ⇒ Object

  An enhancer bound by a factor.

• .enhancer_trap_construct ⇒ Object

  An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements.

• .enhancerRNA ⇒ Object

  A short ncRNA that is transcribed from an enhancer.

• .enzymatic ⇒ Object

  An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein.

• .enzymatic_RNA ⇒ Object

  An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.

• .epigenetically_modified ⇒ Object

  This attribute describes a gene where heritable changes other than those in the DNA sequence occur.

• .epigenetically_modified_gene ⇒ Object

  A gene that is epigenetically modified.

• .epigenetically_modified_region ⇒ Object

  A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence.

• .episome ⇒ Object

  A plasmid that may integrate with a chromosome.

• .epitope ⇒ Object

  A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells.

• .epoxyqueuosine ⇒ Object

  Epoxyqueuosine is a modified 7-deazoguanosine.

• .ER_retention_signal ⇒ Object

  A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum.

• .EST ⇒ Object

  A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.

• .EST_match ⇒ Object

  A match against an EST sequence.

• .eukaryotic_terminator ⇒ Object

  -- No comment or description provided.

• .evidence_for_feature ⇒ Object

  B is evidence_for_feature A, if an instance of B supports the existence of A.

• .exemplar ⇒ Object

  An attribute describing a sequence is representative of a class of similar sequences.

• .exemplar_mRNA ⇒ Object

  An exemplar is a representative cDNA sequence for each gene.

• .exemplar_of ⇒ Object

  X is exemplar of Y if X is the best evidence for Y.

• .exon ⇒ Object

  A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.

• .exon_junction ⇒ Object

  The boundary between two exons in a processed transcript.

• .exon_loss_variant ⇒ Object

  A sequence variant whereby an exon is lost from the transcript.

• .exon_of_single_exon_gene ⇒ Object

  An exon that is the only exon in a gene.

• .exon_region ⇒ Object

  A region of an exon.

• .exon_variant ⇒ Object

  A sequence variant that changes exon sequence.

• .exonic_splice_enhancer ⇒ Object

  Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron.

• .experimental_feature ⇒ Object

  A region which is the result of some arbitrary experimental procedure.

• .experimental_feature_attribute ⇒ Object

  An attribute of an experimentally derived feature.

• .experimental_result_region ⇒ Object

  A region of sequence implicated in an experimental result.

• .experimentally_defined_binding_region ⇒ Object

  A region that has been implicated in binding although the exact coordinates of binding may be unknown.

• .experimentally_determined ⇒ Object

  Attribute to describe a feature that has been experimentally verified.

• .expressed_sequence_assembly ⇒ Object

  A sequence assembly derived from expressed sequences.

• .expressed_sequence_match ⇒ Object

  A match to an EST or cDNA sequence.

• .extended_cis_splice_site ⇒ Object

  Intronic positions associated with cis-splicing.

• .extended_intronic_splice_region ⇒ Object

  Region of intronic sequence within 10 bases of an exon.

• .extended_intronic_splice_region_variant ⇒ Object

  A sequence variant occurring in the intron, within 10 bases of exon.

• .external_transcribed_spacer_region ⇒ Object

  Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA.

• .extrachromosomal_mobile_genetic_element ⇒ Object

  An MGE that is not integrated into the host chromosome.

• .extramembrane_polypeptide_region ⇒ Object

  Polypeptide region that is localized outside of a lipid bilayer.

• .feature_ablation ⇒ Object

  A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features.

• .feature_amplification ⇒ Object

  A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features.

• .feature_attribute ⇒ Object

  An attribute describing a located_sequence_feature.

• .feature_elongation ⇒ Object

  A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence.

• .feature_fusion ⇒ Object

  A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features.

• .feature_translocation ⇒ Object

  A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features.

• .feature_truncation ⇒ Object

  A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence.

• .feature_variant ⇒ Object

  A sequence variant that falls entirely or partially within a genomic feature.

• .fingerprint_map ⇒ Object

  A fingerprint_map is a physical map composed of restriction fragments.

• .finished_by ⇒ Object

  Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary.

• .finished_genome ⇒ Object

  The status of a whole genome sequence, with less than 1 error per 100,000 base pairs.

• .finishes ⇒ Object

  X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary.

• .five_aminomethyl_two_thiouridine ⇒ Object

  5_aminomethyl_2_thiouridine is a modified uridine base feature.

• .five_carbamoylmethyl_two_prime_O_methyluridine ⇒ Object

  5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature.

• .five_carbamoylmethyluridine ⇒ Object

  5_carbamoylmethyluridine is a modified uridine base feature.

• .five_carboxyhydroxymethyl_uridine ⇒ Object

  5_carboxyhydroxymethyl_uridine is a modified uridine base feature.

• .five_carboxyhydroxymethyl_uridine_methyl_ester ⇒ Object

  5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature.

• .five_carboxymethylaminomethyl_two_prime_O_methyluridine ⇒ Object

  5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature.

• .five_carboxymethylaminomethyl_two_thiouridine ⇒ Object

  5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature.

• .five_carboxymethylaminomethyluridine ⇒ Object

  5_carboxymethylaminomethyluridine is a modified uridine base feature.

• .five_carboxymethyluridine ⇒ Object

  5_carboxymethyluridine is a modified uridine base feature.

• .five_formyl_two_prime_O_methylcytidine ⇒ Object

  5-formyl-2'-O-methylcytidine is a modified cytidine.

• .five_formylcytidine ⇒ Object

  5-formylcytidine is a modified cytidine.

• .five_hydroxymethylcytidine ⇒ Object

  5-hydroxymethylcytidine is a modified cytidine.

• .five_hydroxyuridine ⇒ Object

  5_hydroxyuridine is a modified uridine base feature.

• .five_isopentenylaminomethyl_two_prime_O_methyluridine ⇒ Object

  5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature.

• .five_isopentenylaminomethyl_two_thiouridine ⇒ Object

  5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature.

• .five_isopentenylaminomethyl_uridine ⇒ Object

  5_isopentenylaminomethyl_uridine is a modified uridine base feature.

• .five_methoxycarbonylmethyl_two_prime_O_methyluridine ⇒ Object

  Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature.

• .five_methoxycarbonylmethyl_two_thiouridine ⇒ Object

  5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature.

• .five_methoxycarbonylmethyluridine ⇒ Object

  Five_methoxycarbonylmethyluridine is a modified uridine base feature.

• .five_methoxyuridine ⇒ Object

  5_methoxyuridine is a modified uridine base feature.

• .five_methyl_2_thiouridine ⇒ Object

  5_methyl_2_thiouridine is a modified uridine base feature.

• .five_methylaminomethyl_two_selenouridine ⇒ Object

  5_methylaminomethyl_2_selenouridine is a modified uridine base feature.

• .five_methylaminomethyl_two_thiouridine ⇒ Object

  5_methylaminomethyl_2_thiouridine is a modified uridine base feature.

• .five_methylaminomethyluridine ⇒ Object

  5_methylaminomethyluridine is a modified uridine base feature.

• .five_methylcytidine ⇒ Object

  5-methylcytidine is a modified cytidine.

• .five_methyldihydrouridine ⇒ Object

  5_methyldihydrouridine is a modified uridine base feature.

• .five_methyluridine ⇒ Object

  5_methyluridine is a modified uridine base feature.

• .five_prime_cis_splice_site ⇒ Object

  Intronic 2 bp region bordering the exon, at the 5' edge of the intron.

• .five_prime_clip ⇒ Object

  5' most region of a precursor transcript that is clipped off during processing.

• .five_prime_coding_exon ⇒ Object

  The 5' most coding exon.

• .five_prime_coding_exon_coding_region ⇒ Object

  The sequence of the five_prime_coding_exon that codes for protein.

• .five_prime_coding_exon_noncoding_region ⇒ Object

  The sequence of the 5' exon preceding the start codon.

• .five_prime_D_heptamer ⇒ Object

  7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.

• .five_prime_D_nonamer ⇒ Object

  9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.

• .five_prime_D_recombination_signal_sequence ⇒ Object

  Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene.

• .five_prime_D_spacer ⇒ Object

  12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.

• .five_prime_EST ⇒ Object

  An EST read from the 5' end of a transcript that usually codes for a protein.

• .five_prime_five_prime_overlap ⇒ Object

  An attribute to describe a gene when the five prime region overlaps with another gene's five prime region.

• .five_prime_flanking_region ⇒ Object

  A flanking region located five prime of a specific region.

• .five_prime_intron ⇒ Object

  -- No comment or description provided.

• .five_prime_LTR ⇒ Object

  -- No comment or description provided.

• .five_prime_LTR_component ⇒ Object

  -- No comment or description provided.

• .five_prime_noncoding_exon ⇒ Object

  Non-coding exon in the 5' UTR.

• .five_prime_open_reading_frame ⇒ Object

  -- No comment or description provided.

• .five_prime_recoding_site ⇒ Object

  The recoding stimulatory signal located upstream of the recoding site.

• .five_prime_restriction_enzyme_junction ⇒ Object

  The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence.

• .five_prime_RST ⇒ Object

  A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long.

• .five_prime_sticky_end_restriction_enzyme_cleavage_site ⇒ Object

  A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs.

• .five_prime_terminal_inverted_repeat ⇒ Object

  -- No comment or description provided.

• .five_prime_three_prime_overlap ⇒ Object

  An attribute to describe a gene when the five prime region overlaps with another gene's 3' region.

• .five_prime_UST ⇒ Object

  An UST located in the 5'UTR of a protein-coding transcript.

• .five_prime_UTR ⇒ Object

  A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.

• .five_prime_UTR_intron ⇒ Object

  An intron located in the 5' UTR.

• .five_prime_UTR_premature_start_codon_location_variant ⇒ Object

  A 5' UTR variant where a premature start codon is moved.

• .five_taurinomethyl_two_thiouridine ⇒ Object

  5_taurinomethyl_2_thiouridineis a modified uridine base feature.

• .five_taurinomethyluridine ⇒ Object

  5_taurinomethyluridine is a modified uridine base feature.

• .five_two_prime_O_dimethylcytidine ⇒ Object

  5,2'-O-dimethylcytidine is a modified cytidine.

• .five_two_prime_O_dimethyluridine ⇒ Object

  5_2_prime_O_dimethyluridine is a modified uridine base feature.

• .fixed_variant ⇒ Object

  -- No comment or description provided.

• .flanked ⇒ Object

  An attribute describing a region that is bounded either side by a particular kind of region.

• .flanking_region ⇒ Object

  The sequences extending on either side of a specific region.

• .flanking_three_prime_quadruplet_recoding_signal ⇒ Object

  Four base pair sequence immediately downstream of the redefined region.

• .FLEX_element ⇒ Object

  A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain.

• .floxed ⇒ Object

  An attribute describing sequence that is flanked by Lox-P sites.

• .floxed_gene ⇒ Object

  A transgene that is floxed.

• .foldback_element ⇒ Object

  A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats.

• .foreign ⇒ Object

  An attribute to describe a region from another species.

• .foreign_gene ⇒ Object

  A gene that is foreign.

• .foreign_transposable_element ⇒ Object

  A transposable element that is foreign.

• .forkhead_motif ⇒ Object

  A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain.

• .forward ⇒ Object

  Forward is an attribute of the feature, where the feature is in the 5' to 3' direction.

• .forward_primer ⇒ Object

  A single stranded oligo used for polymerase chain reaction.

• .fosmid ⇒ Object

  A cloning vector that utilizes the E.

• .fosmid_clone ⇒ Object

  -- No comment or description provided.

• .four_bp_start_codon ⇒ Object

  A non-canonical start codon with 4 base pairs.

• .four_cutter_restriction_site ⇒ Object

  -- No comment or description provided.

• .four_demethylwyosine ⇒ Object

  4_demethylwyosine is a modified guanosine base feature.

• .four_thiouridine ⇒ Object

  4_thiouridine is a modified uridine base feature.

• .fragment_assembly ⇒ Object

  A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences.

• .fragmentary ⇒ Object

  An attribute to describe a feature that is incomplete.

• .frame_restoring_sequence_variant ⇒ Object

  A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame.

• .frame_restoring_variant ⇒ Object

  A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame.

• .frameshift ⇒ Object

  An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3.

• .frameshift_elongation ⇒ Object

  A frameshift variant that causes the translational reading frame to be extended relative to the reference feature.

• .frameshift_sequence_variation ⇒ Object

  A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.

• .frameshift_truncation ⇒ Object

  A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature.

• .frameshift_variant ⇒ Object

  A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.

• .free ⇒ Object

  The quality of a duplication where the new region exists independently of the original.

• .free_chromosome_arm ⇒ Object

  A chromosome structure variation whereby an arm exists as an individual chromosome element.

• .free_duplication ⇒ Object

  A chromosome structure variation whereby the duplicated sequences are carried as a free centric element.

• .free_ring_duplication ⇒ Object

  A ring chromosome which is a copy of another chromosome.

• .FRT_flanked ⇒ Object

  An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT.

• .FRT_site ⇒ Object

  An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid.

• .functional_candidate_gene ⇒ Object

  A candidate gene whose function has something in common biologically with the trait under investigation.

• .functional_variant ⇒ Object

  A sequence variant in which the function of a gene product is altered with respect to a reference.

• .fusion ⇒ Object

  -- No comment or description provided.

• .fusion_gene ⇒ Object

  A gene that is a fusion.

• .G_box ⇒ Object

  A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG.

• .G_quartet ⇒ Object

  G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet.

• .G_to_A_transition ⇒ Object

  A transition of a guanine to an adenine.

• .G_to_C_transversion ⇒ Object

  A transversion from guanine to cytidine.

• .G_to_T_transversion ⇒ Object

  A transversion from guanine to thymine.

• .GAGA_motif ⇒ Object

  A non directional promoter motif with consensus sequence GAGAGCG.

• .gained ⇒ Object

  X gained Y if X is a variant_of X' and Y part of X but not X'.

• .galactosyl_queuosine ⇒ Object

  Galactosyl_queuosine is a modified 7-deazoguanosine.

• .gamma_turn ⇒ Object

  Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees.

• .gamma_turn_classic ⇒ Object

  Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0.

• .gamma_turn_inverse ⇒ Object

  Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0.

• .gap ⇒ Object

  A gap in the sequence of known length.

• .GATA_box ⇒ Object

  A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G).

• .GC_rich_promoter_region ⇒ Object

  A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG.

• .GcvB_RNA ⇒ Object

  A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.

• .gene ⇒ Object

  A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript.

• .gene_array ⇒ Object

  An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so.

• .gene_array_member ⇒ Object

  -- No comment or description provided.

• .gene_attribute ⇒ Object

  -- No comment or description provided.

• .gene_by_genome_location ⇒ Object

  -- No comment or description provided.

• .gene_by_organelle_of_genome ⇒ Object

  -- No comment or description provided.

• .gene_by_polyadenylation_attribute ⇒ Object

  -- No comment or description provided.

• .gene_by_transcript_attribute ⇒ Object

  This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s).

• .gene_cassette ⇒ Object

  A gene that can be substituted for a related gene at a different site in the genome.

• .gene_cassette_array ⇒ Object

  An array of non-functional genes whose members, when captured by recombination form functional genes.

• .gene_cassette_member ⇒ Object

  -- No comment or description provided.

• .gene_class ⇒ Object

  -- No comment or description provided.

• .gene_component_region ⇒ Object

  -- No comment or description provided.

• .gene_fragment ⇒ Object

  This term is mapped to MGED.

• .gene_fusion ⇒ Object

  A sequence variant whereby a two genes have become joined.

• .gene_group ⇒ Object

  A collection of related genes.

• .gene_group_regulatory_region ⇒ Object

  -- No comment or description provided.

• .gene_member_region ⇒ Object

  A region of a gene.

• .gene_not_polyadenylated ⇒ Object

  -- No comment or description provided.

• .gene_part ⇒ Object

  A part of a gene, that has no other route in the ontology back to region.

• .gene_rearranged_at_DNA_level ⇒ Object

  An epigenetically modified gene, rearranged at the DNA level.

• .gene_segment ⇒ Object

  A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination.

• .gene_sensu_your_favorite_organism ⇒ Object

  -- No comment or description provided.

• .gene_silenced_by_DNA_methylation ⇒ Object

  A gene that is silenced by DNA methylation.

• .gene_silenced_by_DNA_modification ⇒ Object

  A gene that is silenced by DNA modification.

• .gene_silenced_by_histone_deacetylation ⇒ Object

  A gene that is silenced by histone deacetylation.

• .gene_silenced_by_histone_methylation ⇒ Object

  A gene that is silenced by histone methylation.

• .gene_silenced_by_histone_modification ⇒ Object

  A gene that is silenced by histone modification.

• .gene_silenced_by_RNA_interference ⇒ Object

  A gene that is silenced by RNA interference.

• .gene_subarray ⇒ Object

  A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function.

• .gene_subarray_member ⇒ Object

  -- No comment or description provided.

• .gene_to_gene_feature ⇒ Object

  -- No comment or description provided.

• .gene_trap_construct ⇒ Object

  A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct.

• .gene_variant ⇒ Object

  A sequence variant where the structure of the gene is changed.

• .gene_with_dicistronic_mRNA ⇒ Object

  A gene that encodes a polycistronic mRNA.

• .gene_with_dicistronic_primary_transcript ⇒ Object

  A gene that encodes a dicistronic primary transcript.

• .gene_with_dicistronic_transcript ⇒ Object

  A gene that encodes a dicistronic transcript.

• .gene_with_edited_transcript ⇒ Object

  A gene that encodes a transcript that is edited.

• .gene_with_mRNA_recoded_by_translational_bypass ⇒ Object

  A gene with mRNA recoded by translational bypass.

• .gene_with_mRNA_with_frameshift ⇒ Object

  A gene that encodes an mRNA with a frameshift.

• .gene_with_non_canonical_start_codon ⇒ Object

  A gene with a start codon other than AUG.

• .gene_with_polyadenylated_mRNA ⇒ Object

  A gene that encodes a polyadenylated mRNA.

• .gene_with_polycistronic_transcript ⇒ Object

  A gene that encodes a polycistronic transcript.

• .gene_with_recoded_mRNA ⇒ Object

  A gene that encodes an mRNA that is recoded.

• .gene_with_start_codon_CUG ⇒ Object

  A gene with a translational start codon of CUG.

• .gene_with_stop_codon_read_through ⇒ Object

  A gene that encodes a transcript with stop codon readthrough.

• .gene_with_stop_codon_redefined_as_pyrrolysine ⇒ Object

  A gene encoding an mRNA that has the stop codon redefined as pyrrolysine.

• .gene_with_stop_codon_redefined_as_selenocysteine ⇒ Object

  A gene encoding an mRNA that has the stop codon redefined as selenocysteine.

• .gene_with_trans_spliced_transcript ⇒ Object

  A gene with a transcript that is trans-spliced.

• .gene_with_transcript_with_translational_frameshift ⇒ Object

  A gene encoding a transcript that has a translational frameshift.

• .genetic_marker ⇒ Object

  A measurable sequence feature that varies within a population.

• .genome ⇒ Object

  A genome is the sum of genetic material within a cell or virion.

• .genome_of ⇒ Object

  -- No comment or description provided.

• .genomic_clone ⇒ Object

  A clone of a DNA region of a genome.

• .genomic_DNA ⇒ Object

  This term is mapped to MGED.

• .genomic_DNA_read ⇒ Object

  A sequencer read of a genomic DNA substrate.

• .genomic_island ⇒ Object

  A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb).

• .genomically_contaminated_cDNA_clone ⇒ Object

  A cDNA clone invalidated by genomic contamination.

• .genomically_imprinted ⇒ Object

  Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin.

• .genotype ⇒ Object

  A genotype is a variant genome, complete or incomplete.

• .germline_variant ⇒ Object

  -- No comment or description provided.

• .glutamic_acid ⇒ Object

  A place holder for a cross product with chebi.

• .glutamic_acid_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding glutaminyl tRNA (SO:0000260).

• .glutamine ⇒ Object

  A place holder for a cross product with chebi.

• .glutamine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding glutamyl tRNA (SO:0000260).

• .glutaminyl_tRNA ⇒ Object

  A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region.

• .glutamyl_tRNA ⇒ Object

  A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.

• .glycine ⇒ Object

  A place holder for a cross product with chebi.

• .glycine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding glycyl tRNA (SO:0000263).

• .glycyl_tRNA ⇒ Object

  A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.

• .GNA ⇒ Object

  An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone.

• .GNA_oligo ⇒ Object

  An oligo composed of GNA residues.

• .golden_path ⇒ Object

  A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence.

• .golden_path_fragment ⇒ Object

  One of the pieces of sequence that make up a golden path.

• .gRNA_encoding ⇒ Object

  A non-protein_coding gene that encodes a guide_RNA.

• .gRNA_gene ⇒ Object

  -- No comment or description provided.

• .group_1_intron_homing_endonuclease_target_region ⇒ Object

  A region of intronic nucleotide sequence targeted by a nuclease enzyme.

• .group_I_intron ⇒ Object

  Group I catalytic introns are large self-splicing ribozymes.

• .group_II_intron ⇒ Object

  Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria.

• .group_IIA_intron ⇒ Object

  -- No comment or description provided.

• .group_IIB_intron ⇒ Object

  -- No comment or description provided.

• .group_III_intron ⇒ Object

  Group III introns are introns found in the mRNA of the plastids of euglenoid protists.

• .GT_dinucleotide_repeat ⇒ Object

  A dinucleotide repeat region composed of GT repeating elements.

• .GTT_trinucleotide_repeat ⇒ Object

  A trinucleotide repeat region composed of GTT repeating elements.

• .guide_RNA ⇒ Object

  A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.

• .guide_RNA_region ⇒ Object

  A region of guide RNA.

• .guided_by ⇒ Object

  -- No comment or description provided.

• .guides ⇒ Object

  -- No comment or description provided.

• .H2AK5_acetylation_site ⇒ Object

  A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated.

• .H2AK9_acetylation_site ⇒ Object

  A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated.

• .H2B_ubiquitination_site ⇒ Object

  A histone modification site on H2B where ubiquitin may be added.

• .H2BK120_acetylation_site ⇒ Object

  A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated.

• .H2BK12_acetylation_site ⇒ Object

  A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated.

• .H2BK15_acetylation_site ⇒ Object

  A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated.

• .H2BK20_acetylation_site ⇒ Object

  A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated.

• .H2BK5_monomethylation_site ⇒ Object

  A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated.

• .H3K14_acetylation_site ⇒ Object

  A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated.

• .H3K18_acetylation_site ⇒ Object

  A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated.

• .H3K20_trimethylation_site ⇒ Object

  A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated.

• .H3K23_acylation_site ⇒ Object

  A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated.

• .H3K23_dimethylation_site ⇒ Object

  A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated.

• .H3K27_acylation_site ⇒ Object

  A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated.

• .H3K27_dimethylation_site ⇒ Object

  A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated.

• .H3K27_methylation_site ⇒ Object

  A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated.

• .H3K27_monomethylation_site ⇒ Object

  A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated.

• .H3K27_trimethylation_site ⇒ Object

  A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated.

• .H3K36_acetylation_site ⇒ Object

  A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated.

• .H3K36_dimethylation_site ⇒ Object

  A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated.

• .H3K36_methylation_site ⇒ Object

  A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated.

• .H3K36_monomethylation_site ⇒ Object

  A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated.

• .H3K36_trimethylation_site ⇒ Object

  A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated.

• .H3K4_dimethylation_site ⇒ Object

  A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated.

• .H3K4_methylation_site ⇒ Object

  A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated.

• .H3K4_monomethylation_site ⇒ Object

  A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated.

• .H3K4_trimethylation ⇒ Object

  A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated.

• .H3K4ac_acetylation_site ⇒ Object

  A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated.

• .H3K56_acetylation_site ⇒ Object

  A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated.

• .H3K79_dimethylation_site ⇒ Object

  A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated.

• .H3K79_methylation_site ⇒ Object

  A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated.

• .H3K79_monomethylation_site ⇒ Object

  A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated.

• .H3K79_trimethylation_site ⇒ Object

  A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated.

• .H3K9_acetylation_site ⇒ Object

  A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated.

• .H3K9_dimethylation_site ⇒ Object

  A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated.

• .H3K9_methylation_site ⇒ Object

  A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated.

• .H3K9_monomethylation_site ⇒ Object

  A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated.

• .H3K9_trimethylation_site ⇒ Object

  A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated.

• .H3R2_dimethylation_site ⇒ Object

  A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated.

• .H3R2_monomethylation_site ⇒ Object

  A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated.

• .H4K12_acetylation_site ⇒ Object

  A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated.

• .H4K16_acylation_site ⇒ Object

  A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated.

• .H4K20_monomethylation_site ⇒ Object

  A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated.

• .H4K4_trimethylation_site ⇒ Object

  A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated.

• .H4K5_acylation_site ⇒ Object

  A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated.

• .H4K8_acylation_site ⇒ Object

  A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated.

• .H4K91_acetylation_site ⇒ Object

  A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated.

• .H4K_acylation_region ⇒ Object

  A region of the H4 histone whereby multiple lysines are acylated.

• .H4R3_dimethylation_site ⇒ Object

  A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated.

• .H_ACA_box_snoRNA ⇒ Object

  Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule.

• .H_ACA_box_snoRNA_encoding ⇒ Object

  -- No comment or description provided.

• .H_ACA_box_snoRNA_primary_transcript ⇒ Object

  A primary transcript encoding a small nucleolar RNA of the box H/ACA family.

• .H_pseudoknot ⇒ Object

  A pseudoknot which contains two stems and at least two loops.

• .hammerhead_ribozyme ⇒ Object

  A small catalytic RNA motif that catalyzes self-cleavage reaction.

• .haplotype ⇒ Object

  A haplotype is one of a set of coexisting sequence variants of a haplotype block.

• .haplotype_block ⇒ Object

  A region of the genome which is co-inherited as the result of the lack of historic recombination within it.

• .has_integral_part ⇒ Object

  X has_integral_part Y if and only if: X has_part Y and Y part_of X.

• .has_origin ⇒ Object

  -- No comment or description provided.

• .has_parent?(uri, parent) ⇒ Boolean

  Recursively tries to determine the parent for a given URI.

• .has_part ⇒ Object

  Inverse of part_of.

• .has_quality ⇒ Object

  The relationship between a feature and an attribute.

• .helitron ⇒ Object

  A rolling circle transposon.

• .helix_turn_helix ⇒ Object

  A motif comprising two helices separated by a turn.

• .heptamer_of_recombination_feature_of_vertebrate_immune_system_gene ⇒ Object

  Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene.

• .heritable_phenotypic_marker ⇒ Object

  A biological_region characterized as a single heritable trait in a phenotype screen.

• .hetero_compound_chromosome ⇒ Object

  A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them.

• .high_identity_region ⇒ Object

  An experimental feature with high sequence identity to another sequence.

• .high_quality_draft ⇒ Object

  The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome.

• .histidine ⇒ Object

  A place holder for a cross product with chebi.

• .histidine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding histidyl tRNA (SO:0000262).

• .histidyl_tRNA ⇒ Object

  A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.

• .histone_3_acetylation_site ⇒ Object

  A histone 3 modification where the modification is the acylation of the residue.

• .histone_4_acylation_site ⇒ Object

  A histone 4 modification where the modification is the acylation of the residue.

• .histone_acetylation_site ⇒ Object

  A histone modification where the modification is the acylation of the residue.

• .histone_acylation_region ⇒ Object

  A histone modification, whereby the histone protein is acylated at multiple sites in a region.

• .histone_binding_site ⇒ Object

  A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone.

• .histone_methylation_site ⇒ Object

  A histone modification site where the modification is the methylation of the residue.

• .histone_modification ⇒ Object

  Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation.

• .histone_ubiqitination_site ⇒ Object

  A histone modification site where ubiquitin may be added.

• .homing_endonuclease_binding_site ⇒ Object

  The binding site (recognition site) of a homing endonuclease.

• .homo_compound_chromosome ⇒ Object

  A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere.

• .homol_D_box ⇒ Object

  A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence.

• .homol_E_box ⇒ Object

  A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence.

• .homologous ⇒ Object

  Similarity due to common ancestry.

• .homologous_region ⇒ Object

  A region that is homologous to another region.

• .homologous_to ⇒ Object

  -- No comment or description provided.

• .Hoogsteen_base_pair ⇒ Object

  A type of non-canonical base-pairing.

• .HSE ⇒ Object

  A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF.

• .hydrophobic_region_of_peptide ⇒ Object

  Hydrophobic regions are regions with a low affinity for water.

• .hydroxywybutosine ⇒ Object

  Hydroxywybutosine is a modified guanosine base feature.

• .hyperploid ⇒ Object

  A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present.

• .hypoploid ⇒ Object

  A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing.

• .I_box ⇒ Object

  A plant regulatory promoter motif, composed of a highly conserved hexamer GATAAG (I-box core).

• .i_motif ⇒ Object

  A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH.

• .iDNA ⇒ Object

  Genomic sequence removed from the genome, as a normal event, by a process of recombination.

• .immature_peptide_region ⇒ Object

  An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs.

• .immunoglobulin_region ⇒ Object

  A region of immunoglobulin sequence, either constant or variable.

• .improved_high_quality_draft ⇒ Object

  The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution.

• .inactive_catalytic_site ⇒ Object

  A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence.

• .inactive_ligand_binding_site ⇒ Object

  A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence.

• .incomplete_terminal_codon_variant ⇒ Object

  A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed.

• .increased_polyadenylation_variant ⇒ Object

  A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference.

• .increased_transcript_level_variant ⇒ Object

  A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence.

• .increased_transcript_stability_variant ⇒ Object

  A sequence variant that increases transcript stability with respect to a reference sequence.

• .increased_transcription_rate_variant ⇒ Object

  A sequence variant that increases the rate of transcription with respect to a reference sequence.

• .increased_translational_product_level ⇒ Object

  A sequence variant which increases the translational product level with respect to a reference sequence.

• .indel ⇒ Object

  A sequence alteration which included an insertion and a deletion, affecting 2 or more bases.

• .independently_known ⇒ Object

  Attribute to describe a feature that is independently known - not predicted.

• .inframe ⇒ Object

  An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3.

• .inframe_deletion ⇒ Object

  An inframe non synonymous variant that deletes bases from the coding sequence.

• .inframe_indel ⇒ Object

  A coding sequence variant where the change does not alter the frame of the transcript.

• .inframe_insertion ⇒ Object

  An inframe non synonymous variant that inserts bases into in the coding sequence.

• .inframe_variant ⇒ Object

  A sequence variant which does not cause a disruption of the translational reading frame.

• .initiator_codon_variant ⇒ Object

  A codon variant that changes at least one base of the first codon of a transcript.

• .inosine ⇒ Object

  A modified RNA base in which hypoxanthine is bound to the ribose ring.

• .INR1_motif ⇒ Object

  A promoter motif with consensus sequence TCATTCG.

• .INR_motif ⇒ Object

  A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription.

• .insert ⇒ Object

  To insert a subsection of sequence.

• .insert_AA ⇒ Object

  An edit to insert a AA dinucleotide.

• .insert_AU ⇒ Object

  An edit to insert a AU dinucleotide.

• .insert_C ⇒ Object

  An edit to insert a cytidine.

• .insert_CU ⇒ Object

  An edit to insert a CU dinucleotide.

• .insert_dinucleotide ⇒ Object

  An edit to insert a dinucleotide.

• .insert_G ⇒ Object

  An edit to insert a G.

• .insert_GC ⇒ Object

  An edit to insert a GC dinucleotide.

• .insert_GU ⇒ Object

  An edit to insert a GU dinucleotide.

• .insert_U ⇒ Object

  An edit to insert a U.

• .insertion ⇒ Object

  The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.

• .insertion_attribute ⇒ Object

  A quality of a chromosomal insertion,.

• .insertion_breakpoint ⇒ Object

  The point within a chromosome where a insertion begins or ends.

• .insertion_sequence ⇒ Object

  A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats.

• .insertion_site ⇒ Object

  The junction where an insertion occurred.

• .insertional ⇒ Object

  -- No comment or description provided.

• .insertional_duplication ⇒ Object

  A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication).

• .inside_intron ⇒ Object

  An attribute to describe a gene when it is located within the intron of another gene.

• .inside_intron_antiparallel ⇒ Object

  An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand.

• .inside_intron_parallel ⇒ Object

  An attribute to describe a gene when it is located within the intron of another gene and on the same strand.

• .insulator ⇒ Object

  A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression.

• .insulator_binding_site ⇒ Object

  A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.

• .integral_part_of ⇒ Object

  X integral_part_of Y if and only if: X part_of Y and Y has_part X.

• .integrase_coding_region ⇒ Object

  -- No comment or description provided.

• .integrated_mobile_genetic_element ⇒ Object

  An MGE that is integrated into the host chromosome.

• .integrated_plasmid ⇒ Object

  A plasmid sequence that is integrated within the host chromosome.

• .integration_excision_site ⇒ Object

  A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site.

• .integron ⇒ Object

  A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site.

• .intein ⇒ Object

  A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond.

• .intein_containing ⇒ Object

  An attribute of protein-coding genes where the initial protein product contains an intein.

• .interband ⇒ Object

  A light region between two darkly staining bands in a polytene chromosome.

• .interchromosomal ⇒ Object

  -- No comment or description provided.

• .interchromosomal_breakpoint ⇒ Object

  A rearrangement breakpoint between two different chromosomes.

• .interchromosomal_duplication ⇒ Object

  A chromosome duplication involving an insertion from another chromosome.

• .interchromosomal_mutation ⇒ Object

  A chromosomal structure variation whereby more than one chromosome is involved.

• .interchromosomal_transposition ⇒ Object

  A chromosome structure variation whereby a transposition occurred between chromosomes.

• .intergenic_region ⇒ Object

  A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome.

• .intergenic_variant ⇒ Object

  A sequence variant located in the intergenic region, between genes.

• .interior_coding_exon ⇒ Object

  -- No comment or description provided.

• .interior_exon ⇒ Object

  An exon that is bounded by 5' and 3' splice sites.

• .interior_intron ⇒ Object

  -- No comment or description provided.

• .intermediate ⇒ Object

  An attribute to describe a feature between stages of processing.

• .intermediate_element ⇒ Object

  A core promoter region of RNA polymerase III type 1 promoters.

• .internal_eliminated_sequence ⇒ Object

  A sequence eliminated from the genome of ciliates during nuclear differentiation.

• .internal_feature_elongation ⇒ Object

  A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence.

• .internal_guide_sequence ⇒ Object

  A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity.

• .internal_ribosome_entry_site ⇒ Object

  Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation.

• .internal_Shine_Dalgarno_sequence ⇒ Object

  A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes.

• .internal_transcribed_spacer_region ⇒ Object

  Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs.

• .internal_UTR ⇒ Object

  A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript.

• .intrachromosomal ⇒ Object

  -- No comment or description provided.

• .intrachromosomal_breakpoint ⇒ Object

  A rearrangement breakpoint within the same chromosome.

• .intrachromosomal_duplication ⇒ Object

  A duplication that occurred within a chromosome.

• .intrachromosomal_mutation ⇒ Object

  A chromosomal structure variation within a single chromosome.

• .intrachromosomal_transposition ⇒ Object

  A chromosome structure variation whereby a transposition occurred within a chromosome.

• .intramembrane_polypeptide_region ⇒ Object

  Polypeptide region present in the lipid bilayer.

• .intrinsically_unstructured_polypeptide_region ⇒ Object

  A region of polypeptide chain with high conformational flexibility.

• .introgressed_chromosome_region ⇒ Object

  -- No comment or description provided.

• .intron ⇒ Object

  A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.

• .intron_attribute ⇒ Object

  -- No comment or description provided.

• .intron_base_5 ⇒ Object

  Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron.

• .intron_domain ⇒ Object

  Requested by Colin Batchelor, Feb 2007.

• .intron_gain ⇒ Object

  A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor.

• .intron_variant ⇒ Object

  A transcript variant occurring within an intron.

• .intronic_lncRNA ⇒ Object

  A lnc_RNA totally contained within an intron.

• .intronic_regulatory_region ⇒ Object

  A regulatory region that is part of an intron.

• .intronic_splice_enhancer ⇒ Object

  Sequences within the intron that modulate splice site selection for some introns.

• .invalidated ⇒ Object

  An attribute describing a feature that is invalidated.

• .invalidated_by_chimeric_cDNA ⇒ Object

  A cDNA clone constructed from more than one mRNA.

• .invalidated_by_genomic_contamination ⇒ Object

  An attribute to describe a feature that is invalidated due to genomic contamination.

• .invalidated_by_genomic_polyA_primed_cDNA ⇒ Object

  An attribute to describe a feature that is invalidated due to polyA priming.

• .invalidated_by_partial_processing ⇒ Object

  An attribute to describe a feature that is invalidated due to partial processing.

• .invalidated_cDNA_clone ⇒ Object

  A cDNA clone that is invalid.

• .inversion ⇒ Object

  A continuous nucleotide sequence is inverted in the same position.

• .inversion_attribute ⇒ Object

  -- No comment or description provided.

• .inversion_breakpoint ⇒ Object

  The point within a chromosome where an inversion begins or ends.

• .inversion_cum_translocation ⇒ Object

  A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome.

• .inversion_derived_aneuploid_chromosome ⇒ Object

  A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion.

• .inversion_derived_bipartite_deficiency ⇒ Object

  A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion.

• .inversion_derived_bipartite_duplication ⇒ Object

  A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion.

• .inversion_derived_deficiency_plus_aneuploid ⇒ Object

  A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion.

• .inversion_derived_deficiency_plus_duplication ⇒ Object

  A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion.

• .inversion_derived_duplication_plus_aneuploid ⇒ Object

  A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion.

• .inversion_site ⇒ Object

  A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites.

• .inversion_site_part ⇒ Object

  A region located within an inversion site.

• .invert ⇒ Object

  To invert a subsection of sequence.

• .inverted ⇒ Object

  A quality of an insertion where the insert is in a cytologically inverted orientation.

• .inverted_insertional_duplication ⇒ Object

  An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments.

• .inverted_interchromosomal_transposition ⇒ Object

  An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment.

• .inverted_intrachromosomal_transposition ⇒ Object

  An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments.

• .inverted_repeat ⇒ Object

  The sequence is complementarily repeated on the opposite strand.

• .inverted_ring_chromosome ⇒ Object

  -- No comment or description provided.

• .inverted_tandem_duplication ⇒ Object

  A tandem duplication where the individual regions are not in the same orientation.

• .IRLinv_site ⇒ Object

  Component of the inversion site located at the left of a region susceptible to site-specific inversion.

• .iron_repressed_GATA_element ⇒ Object

  A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron.

• .iron_responsive_element ⇒ Object

  A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins.

• .IRRinv_site ⇒ Object

  Component of the inversion site located at the right of a region susceptible to site-specific inversion.

• .is_class?(uri) ⇒ Boolean

  Determines whether the given URI is a class.

• .is_consecutive_sequence_of ⇒ Object

  R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical).

• .is_datatype_property?(uri) ⇒ Boolean

  Determines whether the given URI is a datatype property.

• .is_named_individual?(uri) ⇒ Boolean

  Determines whether the given URI is a named individual.

• .is_object_property?(uri) ⇒ Boolean

  Determines whether the given URI is an object property.

• .isoleucine ⇒ Object

  A place holder for a cross product with chebi.

• .isoleucine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding isoleucyl tRNA (SO:0000263).

• .isoleucyl_tRNA ⇒ Object

  A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.

• .isowyosine ⇒ Object

  Isowyosine is a modified guanosine base feature.

• .ISRE ⇒ Object

  An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding.

• .J_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene.

• .J_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene.

• .J_gene_recombination_feature ⇒ Object

  Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence.

• .J_gene_segment ⇒ Object

  Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment.

• .J_heptamer ⇒ Object

  7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.

• .J_nonamer ⇒ Object

  9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.

• .J_spacer ⇒ Object

  12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.

• .junction ⇒ Object

  A sequence_feature with an extent of zero.

• .K_turn_RNA_motif ⇒ Object

  The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices.

• .KEN_box ⇒ Object

  A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C.

• .kinetoplast ⇒ Object

  A kinetoplast is an interlocked network of thousands of minicircles and tens of maxi circles, located near the base of the flagellum of some protozoan species.

• .kinetoplast_gene ⇒ Object

  A gene located in kinetoplast sequence.

• .kozak_sequence ⇒ Object

  A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.

• .L_box ⇒ Object

  An orientation dependent regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants.

• .laevosynaptic_chromosome ⇒ Object

  LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres.

• .lambda_clone ⇒ Object

  A linear clone derived from lambda bacteriophage.

• .lambda_vector ⇒ Object

  The lambda bacteriophage is the vector for the linear lambda clone.

• .large_subunit_rRNA ⇒ Object

  Ribosomal RNA transcript that structures the large subunit of the ribosome.

• .lariat_intron ⇒ Object

  A kind of intron whereby the excision is driven by lariat formation.

• .left_handed_peptide_helix ⇒ Object

  A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw.

• .lethal_variant ⇒ Object

  -- No comment or description provided.

• .leucine ⇒ Object

  A place holder for a cross product with chebi.

• .leucine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding leucyl tRNA (SO:0000264).

• .leucoplast_chromosome ⇒ Object

  A chromosome with origin in a leucoplast.

• .leucoplast_gene ⇒ Object

  A plastid gene from leucoplast sequence.

• .leucoplast_sequence ⇒ Object

  -- No comment or description provided.

• .leucyl_tRNA ⇒ Object

  A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.

• .level_of_transcript_variant ⇒ Object

  A sequence variant which alters the level of a transcript.

• .ligand_binding_site ⇒ Object

  A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone.

• .ligation_based_read ⇒ Object

  A read produced by ligation based sequencing technologies.

• .lincRNA ⇒ Object

  A multiexonic non-coding RNA transcribed by RNA polymerase II.

• .lincRNA_gene ⇒ Object

  A gene that encodes large intervening non-coding RNA.

• .LINE_element ⇒ Object

  A dispersed repeat family with many copies, each from 1 to 6 kb long.

• .linear ⇒ Object

  A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue.

• .linear_double_stranded_DNA_chromosome ⇒ Object

  Structural unit composed of a self-replicating, double-stranded, linear DNA molecule.

• .linear_double_stranded_RNA_chromosome ⇒ Object

  Structural unit composed of a self-replicating, double-stranded, linear RNA molecule.

• .linear_single_stranded_DNA_chromosome ⇒ Object

  Structural unit composed of a self-replicating, single-stranded, linear DNA molecule.

• .linear_single_stranded_RNA_chromosome ⇒ Object

  Structural unit composed of a self-replicating, single-stranded, linear RNA molecule.

• .linkage_group ⇒ Object

  A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned.

• .lipoprotein_signal_peptide ⇒ Object

  A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes.

• .LNA ⇒ Object

  An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone.

• .LNA_oligo ⇒ Object

  An oligo composed of LNA residues.

• .lnc_RNA ⇒ Object

  A non-coding RNA over 200nucleotides in length.

• .locus_control_region ⇒ Object

  A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene.

• .long_terminal_repeat ⇒ Object

  A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses.

• .loss_of_heterozygosity ⇒ Object

  A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene.

• .lost ⇒ Object

  X lost Y if X is a variant_of X' and Y part of X' but not X.

• .low_complexity ⇒ Object

  -- No comment or description provided.

• .low_complexity_region ⇒ Object

  -- No comment or description provided.

• .loxP_site ⇒ Object

  -- No comment or description provided.

• .LTR_component ⇒ Object

  -- No comment or description provided.

• .LTR_retrotransposon ⇒ Object

  A retrotransposon flanked by long terminal repeat sequences.

• .lysidine ⇒ Object

  Lysidine is a modified cytidine.

• .lysine ⇒ Object

  A place holder for a cross product with chebi.

• .lysine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding lysyl tRNA (SO:0000265).

• .lysosomal_localization_signal ⇒ Object

  A polypeptide region that targets a polypeptide to the lysosome.

• .lysyl_tRNA ⇒ Object

  A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.

• .M26_binding_site ⇒ Object

  A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components.

• .macronuclear_chromosome ⇒ Object

  A chromosome originating in a macronucleus.

• .macronuclear_sequence ⇒ Object

  -- No comment or description provided.

• .macronucleus_destined_segment ⇒ Object

  A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome.

• .major_TSS ⇒ Object

  -- No comment or description provided.

• .mannosyl_queuosine ⇒ Object

  Mannosyl_queuosine is a modified 7-deazoguanosine.

• .match ⇒ Object

  A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.

• .match_part ⇒ Object

  A part of a match, for example an hsp from blast is a match_part.

• .match_set ⇒ Object

  A collection of match parts.

• .maternal_uniparental_disomy ⇒ Object

  Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father.

• .maternal_variant ⇒ Object

  -- No comment or description provided.

• .maternally_imprinted ⇒ Object

  The maternal copy of the gene is modified, rendering it transcriptionally silent.

• .maternally_imprinted_gene ⇒ Object

  A gene that is maternally_imprinted.

• .mathematically_defined_repeat ⇒ Object

  A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness.

• .mating_type_M_box ⇒ Object

  A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc.

• .mating_type_region ⇒ Object

  A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type.

• .mating_type_region_motif ⇒ Object

  DNA motif that is a component of a mating type region.

• .matrix_attachment_site ⇒ Object

  A DNA region that is required for the binding of chromatin to the nuclear matrix.

• .mature_miRNA_variant ⇒ Object

  A transcript variant located with the sequence of the mature miRNA.

• .mature_protein_region ⇒ Object

  The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide.

• .mature_transcript ⇒ Object

  A transcript which has undergone the necessary modifications, if any, for its function.

• .mature_transcript_region ⇒ Object

  A region of a mature transcript.

• .maxicircle ⇒ Object

  A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method.

• .maxicircle_gene ⇒ Object

  A mitochondrial gene located in a maxicircle.

• .maximally_overlaps ⇒ Object

  A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y.

• .MCB ⇒ Object

  A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle.

• .member_of ⇒ Object

  A subtype of part_of.

• .member_of_regulon ⇒ Object

  -- No comment or description provided.

• .membrane_peptide_loop ⇒ Object

  Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane.

• .membrane_structure ⇒ Object

  Arrangement of the polypeptide with respect to the lipid bilayer.

• .metabolic_island ⇒ Object

  A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria.

• .metal_binding_site ⇒ Object

  A binding site that, in the molecule, interacts selectively and non-covalently with metal ions.

• .methionine ⇒ Object

  A place holder for a cross product with chebi.

• .methionine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding methionyl tRNA (SO:0000266).

• .methionyl_tRNA ⇒ Object

  A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.

• .methylated_adenine ⇒ Object

  A modified base in which adenine has been methylated.

• .methylated_cytosine ⇒ Object

  A methylated deoxy-cytosine.

• .methylated_DNA_base_feature ⇒ Object

  A nucleotide modified by methylation.

• .methylation_guide_snoRNA ⇒ Object

  A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue.

• .methylation_guide_snoRNA_primary_transcript ⇒ Object

  A primary transcript encoding a methylation guide small nucleolar RNA.

• .methylinosine ⇒ Object

  A modified RNA base in which methylhypoxanthine is bound to the ribose ring.

• .methylwyosine ⇒ Object

  Methylwyosine is a modified guanosine base feature.

• .MicF_RNA ⇒ Object

  A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message.

• .microarray_oligo ⇒ Object

  -- No comment or description provided.

• .micronuclear_chromosome ⇒ Object

  A chromosome originating in a micronucleus.

• .micronuclear_sequence ⇒ Object

  -- No comment or description provided.

• .microsatellite ⇒ Object

  A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.

• .mini_exon_donor_RNA ⇒ Object

  A primary transcript that donates the spliced leader to other mRNA.

• .mini_gene ⇒ Object

  By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected).

• .minicircle ⇒ Object

  A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs.

• .minicircle_gene ⇒ Object

  -- No comment or description provided.

• .minisatellite ⇒ Object

  A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp.

• .minor_TSS ⇒ Object

  -- No comment or description provided.

• .minus_10_signal ⇒ Object

  A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT.

• .minus_12_signal ⇒ Object

  A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54.

• .minus_1_frameshift ⇒ Object

  A frameshift caused by deleting one base.

• .minus_1_frameshift_variant ⇒ Object

  A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead.

• .minus_1_translationally_frameshifted ⇒ Object

  An attribute describing a translational frameshift of -1.

• .minus_24_signal ⇒ Object

  A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54.

• .minus_2_frameshift ⇒ Object

  A frameshift caused by deleting two bases.

• .minus_2_frameshift_variant ⇒ Object

  -- No comment or description provided.

• .minus_35_signal ⇒ Object

  A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA.

• .miRNA ⇒ Object

  Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene.

• .miRNA_antiguide ⇒ Object

  A region of the pri miRNA that basepairs with the guide to form the hairpin.

• .miRNA_encoding ⇒ Object

  -- No comment or description provided.

• .miRNA_gene ⇒ Object

  -- No comment or description provided.

• .miRNA_loop ⇒ Object

  The loop of the hairpin loop formed by folding of the pre-miRNA.

• .miRNA_primary_transcript ⇒ Object

  A primary transcript encoding a micro RNA.

• .miRNA_primary_transcript_region ⇒ Object

  A part of an miRNA primary_transcript.

• .miRNA_stem ⇒ Object

  The stem of the hairpin loop formed by folding of the pre-miRNA.

• .miRNA_target_site ⇒ Object

  A miRNA target site is a binding site where the molecule is a micro RNA.

• .mirtron ⇒ Object

  A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage.

• .missense_variant ⇒ Object

  A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved.

• .MITE ⇒ Object

  A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD).

• .mitochondrial_chromosome ⇒ Object

  A chromosome originating in a mitochondria.

• .mitochondrial_contig ⇒ Object

  A contig of mitochondria derived sequences.

• .mitochondrial_DNA ⇒ Object

  This terms is used by MO.

• .mitochondrial_DNA_read ⇒ Object

  A sequencer read of a mitochondrial DNA sample.

• .mitochondrial_sequence ⇒ Object

  This term is mapped to MGED.

• .mitochondrial_supercontig ⇒ Object

  A scaffold composed of mitochondrial contigs.

• .mitochondrial_targeting_signal ⇒ Object

  A polypeptide region that targets a polypeptide to the mitochondrion.

• .MNP ⇒ Object

  A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.

• .MNV ⇒ Object

  A multiple nucleotide substitution in which the inserted sequence is the same length as the replaced sequence.

• .mobile ⇒ Object

  An attribute describing a feature that has either intra-genome or intracellular mobility.

• .mobile_element_insertion ⇒ Object

  A kind of insertion where the inserted sequence is a mobile element.

• .mobile_genetic_element ⇒ Object

  A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome.

• .mobile_intron ⇒ Object

  An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility.

• .modified_adenine ⇒ Object

  A modified adenine DNA base feature.

• .modified_adenosine ⇒ Object

  A modified adenine is an adenine base feature that has been altered.

• .modified_amino_acid_feature ⇒ Object

  A post translationally modified amino acid feature.

• .modified_cytidine ⇒ Object

  A modified cytidine is a cytidine base feature which has been altered.

• .modified_cytosine ⇒ Object

  A modified cytosine DNA base feature.

• .modified_DNA_base ⇒ Object

  A modified nucleotide, i.e.

• .modified_glycine ⇒ Object

  A post translationally modified glycine amino acid feature.

• .modified_guanine ⇒ Object

  A modified guanine DNA base feature.

• .modified_guanosine ⇒ Object

  -- No comment or description provided.

• .modified_inosine ⇒ Object

  A modified inosine is an inosine base feature that has been altered.

• .modified_L_alanine ⇒ Object

  A post translationally modified alanine amino acid feature.

• .modified_L_arginine ⇒ Object

  A post translationally modified arginine amino acid feature.

• .modified_L_asparagine ⇒ Object

  A post translationally modified asparagine amino acid feature.

• .modified_L_aspartic_acid ⇒ Object

  A post translationally modified aspartic acid amino acid feature.

• .modified_L_cysteine ⇒ Object

  A post translationally modified cysteine amino acid feature.

• .modified_L_glutamic_acid ⇒ Object

  -- No comment or description provided.

• .modified_L_glutamine ⇒ Object

  A post translationally modified glutamine amino acid feature.

• .modified_L_histidine ⇒ Object

  A post translationally modified histidie amino acid feature.

• .modified_L_isoleucine ⇒ Object

  A post translationally modified isoleucine amino acid feature.

• .modified_L_leucine ⇒ Object

  A post translationally modified leucine amino acid feature.

• .modified_L_lysine ⇒ Object

  A post translationally modified lysine amino acid feature.

• .modified_L_methionine ⇒ Object

  A post translationally modified methionine amino acid feature.

• .modified_L_phenylalanine ⇒ Object

  A post translationally modified phenylalanine amino acid feature.

• .modified_L_proline ⇒ Object

  A post translationally modified proline amino acid feature.

• .modified_L_selenocysteine ⇒ Object

  A post translationally modified selenocysteine amino acid feature.

• .modified_L_serine ⇒ Object

  A post translationally modified serine amino acid feature.

• .modified_L_threonine ⇒ Object

  A post translationally modified threonine amino acid feature.

• .modified_L_tryptophan ⇒ Object

  A post translationally modified tryptophan amino acid feature.

• .modified_L_tyrosine ⇒ Object

  A post translationally modified tyrosine amino acid feature.

• .modified_L_valine ⇒ Object

  A post translationally modified valine amino acid feature.

• .modified_RNA_base_feature ⇒ Object

  A post_transcriptionally modified base.

• .modified_uridine ⇒ Object

  -- No comment or description provided.

• .molecular_contact_region ⇒ Object

  A region that is involved a contact with another molecule.

• .monocistronic ⇒ Object

  An attribute describing a sequence that contains the code for one gene product.

• .monocistronic_mRNA ⇒ Object

  An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.

• .monocistronic_primary_transcript ⇒ Object

  A primary transcript encoding for one gene product.

• .monocistronic_transcript ⇒ Object

  A transcript that is monocistronic.

• .monomeric_repeat ⇒ Object

  A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem.

• .morpholino_backbone ⇒ Object

  An attribute describing a sequence composed of nucleobases bound to a morpholino backbone.

• .morpholino_oligo ⇒ Object

  Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring.

• .mRNA ⇒ Object

  Messenger RNA is the intermediate molecule between DNA and protein.

• .mRNA_attribute ⇒ Object

  An attribute describing an mRNA feature.

• .mRNA_by_polyadenylation_status ⇒ Object

  -- No comment or description provided.

• .mRNA_contig ⇒ Object

  A contig composed of mRNA_reads.

• .mRNA_not_polyadenylated ⇒ Object

  -- No comment or description provided.

• .mRNA_read ⇒ Object

  A sequencer read of an mRNA substrate.

• .mRNA_recoded_by_codon_redefinition ⇒ Object

  A recoded_mRNA that was modified by an alteration of codon meaning.

• .mRNA_recoded_by_translational_bypass ⇒ Object

  A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon.

• .mRNA_region ⇒ Object

  A region of an mRNA.

• .mRNA_with_frameshift ⇒ Object

  An mRNA with a frameshift.

• .mRNA_with_minus_1_frameshift ⇒ Object

  An mRNA with a minus 1 frameshift.

• .mRNA_with_minus_2_frameshift ⇒ Object

  A mRNA with a minus 2 frameshift.

• .mRNA_with_plus_1_frameshift ⇒ Object

  An mRNA with a plus 1 frameshift.

• .mRNA_with_plus_2_frameshift ⇒ Object

  An mRNA with a plus 2 frameshift.

• .mt_gene ⇒ Object

  A gene located in mitochondrial sequence.

• .MTE ⇒ Object

  A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS.

• .mutated_variant_site ⇒ Object

  Site which has been experimentally altered.

• .mutation_causing_inframe_polypeptide_N_terminal_elongation ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .mutation_causing_out_of_frame_polypeptide_C_terminal_elongation ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .mutation_causing_out_of_frame_polypeptide_N_terminal_elongation ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .mutation_causing_polypeptide_C_terminal_elongation ⇒ Object

  . (http://purl.obolibrary.org/obo/SO_1000101).

• .mutation_causing_polypeptide_N_terminal_elongation ⇒ Object

  . (http://purl.obolibrary.org/obo/SO_1000100).

• .mutaton_causing_inframe_polypeptide_C_terminal_elongation ⇒ Object

  -- No comment or description provided.

• .N2_2_prime_O_dimethylguanosine ⇒ Object

  N2_2prime_O_dimethylguanosine is a modified guanosine base feature.

• .N2_7_2prirme_O_trimethylguanosine ⇒ Object

  N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature.

• .N2_7_dimethylguanosine ⇒ Object

  N2_7_dimethylguanosine is a modified guanosine base feature.

• .N2_methylguanosine ⇒ Object

  N2_methylguanosine is a modified guanosine base feature.

• .N2_N2_2_prime_O_trimethylguanosine ⇒ Object

  N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature.

• .N2_N2_7_trimethylguanosine ⇒ Object

  N2_N2_7_trimethylguanosine is a modified guanosine base feature.

• .N2_N2_dimethylguanosine ⇒ Object

  N2_N2_dimethylguanosine is a modified guanosine base feature.

• .N4_2_prime_O_dimethylcytidine ⇒ Object

  N4,2'-O-dimethylcytidine is a modified cytidine.

• .N4_acetyl_2_prime_O_methylcytidine ⇒ Object

  N4-acetyl-2'-O-methylcytidine is a modified cytidine.

• .N4_acetylcytidine ⇒ Object

  N4-acetylcytidine is a modified cytidine.

• .N4_methylcytidine ⇒ Object

  N4-methylcytidine is a modified cytidine.

• .N4_N4_2_prime_O_trimethylcytidine ⇒ Object

  N4_N4_2_prime_O_trimethylcytidine is a modified cytidine.

• .N6_2_prime_O_dimethyladenosine ⇒ Object

  N6_2prime_O_dimethyladenosine is a modified adenosine.

• .N6_acetyladenosine ⇒ Object

  N6_acetyladenosine is a modified adenosine.

• .N6_cis_hydroxyisopentenyl_adenosine ⇒ Object

  N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.

• .N6_glycinylcarbamoyladenosine ⇒ Object

  N6_glycinylcarbamoyladenosine is a modified adenosine.

• .N6_hydroxynorvalylcarbamoyladenosine ⇒ Object

  N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine.

• .N6_isopentenyladenosine ⇒ Object

  N6_isopentenyladenosine is a modified adenosine.

• .N6_methyl_N6_threonylcarbamoyladenosine ⇒ Object

  N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine.

• .N6_methyladenine ⇒ Object

  An adenine methylated at the 6 nitrogen.

• .N6_methyladenosine ⇒ Object

  N6_methyladenosine is a modified adenosine.

• .N6_N6_2_prime_O_trimethyladenosine ⇒ Object

  N6_N6_2prime_O_trimethyladenosine is a modified adenosine.

• .N6_N6_dimethyladenosine ⇒ Object

  N6_N6_dimethyladenosine is a modified adenosine.

• .N6_threonylcarbamoyladenosine ⇒ Object

  N6_threonylcarbamoyladenosine is a modified adenosine.

• .N_region ⇒ Object

  Extra nucleotides inserted between rearranged immunoglobulin segments.

• .n_terminal_region ⇒ Object

  The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa).

• .natural ⇒ Object

  An attribute describing a feature that occurs in nature.

• .natural_plasmid ⇒ Object

  A plasmid that occurs naturally.

• .natural_transposable_element ⇒ Object

  TE that exists (or existed) in nature.

• .natural_variant_site ⇒ Object

  Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars.

• .nc_conserved_region ⇒ Object

  Non-coding region of sequence similarity by descent from a common ancestor.

• .nc_primary_transcript ⇒ Object

  A primary transcript that is never translated into a protein.

• .ncRNA ⇒ Object

  An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.

• .ncRNA_gene ⇒ Object

  -- No comment or description provided.

• .NDM2_motif ⇒ Object

  A non directional promoter motif with consensus CGMYGYCR.

• .NDM3_motif ⇒ Object

  A non directional promoter motif with consensus sequence GAAAGCT.

• .negative_sense_ssRNA_viral_sequence ⇒ Object

  A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation.

• .negatively_autoregulated ⇒ Object

  The gene product is involved in its own transcriptional regulation where it decreases transcription.

• .negatively_autoregulated_gene ⇒ Object

  A gene that is negatively autoreguated.

• .nested_region ⇒ Object

  -- No comment or description provided.

• .nested_repeat ⇒ Object

  Either: -- No comment or description provided.

• .nested_tandem_repeat ⇒ Object

  An NTR is a nested repeat of two distinct tandem motifs interspersed with each other.

• .nested_transposon ⇒ Object

  Either: -- No comment or description provided.

• .NMD_transcript_variant ⇒ Object

  A variant in a transcript that is the target of NMD.

• .no_output ⇒ Object

  An experimental region wherean analysis has been run and not produced any annotation.

• .non_adjacent_residues ⇒ Object

  Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them.

• .non_canonical_five_prime_splice_site ⇒ Object

  A 5' splice site which does not have the sequence "GT".

• .non_canonical_splice_site ⇒ Object

  A splice site where the donor and acceptor sites differ from the canonical form.

• .non_canonical_start_codon ⇒ Object

  A start codon that is not the usual AUG sequence.

• .non_canonical_three_prime_splice_site ⇒ Object

  A 3' splice site that does not have the sequence "AG".

• .non_capped_primary_transcript ⇒ Object

  -- No comment or description provided.

• .non_coding_transcript_exon_variant ⇒ Object

  A sequence variant that changes non-coding exon sequence in a non-coding transcript.

• .non_coding_transcript_intron_variant ⇒ Object

  A transcript variant occurring within an intron of a non coding transcript.

• .non_coding_transcript_variant ⇒ Object

  A transcript variant of a non coding RNA gene.

• .non_conservative_amino_acid_substitution ⇒ Object

  A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide.

• .non_conservative_missense_variant ⇒ Object

  A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties.

• .non_covalent_binding_site ⇒ Object

  Binding site for any chemical group (co-enzyme, prosthetic group, etc.).

• .non_cytoplasmic_polypeptide_region ⇒ Object

  Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm.

• .non_functional_homolog_of ⇒ Object

  A relationship between a pseudogenic feature and its functional ancestor.

• .non_LTR_retrotransposon ⇒ Object

  A retrotransposon without long terminal repeat sequences.

• .non_LTR_retrotransposon_polymeric_tract ⇒ Object

  A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon.

• .non_processed_pseudogene ⇒ Object

  A pseudogene that arose from a means other than retrotransposition.

• .non_protein_coding ⇒ Object

  -- No comment or description provided.

• .non_synonymous ⇒ Object

  -- No comment or description provided.

• .non_terminal_residue ⇒ Object

  The residue at an extremity of the sequence is not the terminal residue.

• .non_transcribed_region ⇒ Object

  A region of the gene which is not transcribed.

• .nonamer_of_recombination_feature_of_vertebrate_immune_system_gene ⇒ Object

  -- No comment or description provided.

• .noncoding_exon ⇒ Object

  An exon that does not contain any codons.

• .noncoding_region_of_exon ⇒ Object

  The maximal intersection of exon and UTR.

• .noncontiguous_finished ⇒ Object

  The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions.

• .nonsynonymous_variant ⇒ Object

  A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change.

• .novel_sequence_insertion ⇒ Object

  An insertion the sequence of which cannot be mapped to the reference genome.

• .nuclear_chromosome ⇒ Object

  A chromosome originating in a nucleus.

• .nuclear_export_signal ⇒ Object

  A polypeptide region that targets a polypeptide to he cytoplasm.

• .nuclear_gene ⇒ Object

  A gene from nuclear sequence.

• .nuclear_localization_signal ⇒ Object

  A polypeptide region that targets a polypeptide to the nucleus.

• .nuclear_mitochondrial ⇒ Object

  An attribute describing a nuclear pseudogene of a mitochndrial gene.

• .nuclear_mt_pseudogene ⇒ Object

  A nuclear pseudogene of either coding or non-coding mitochondria derived sequence.

• .nuclear_rim_localization_signal ⇒ Object

  A polypeptide region that targets a polypeptide to the nuclear rim.

• .nuclear_sequence ⇒ Object

  -- No comment or description provided.

• .nuclease_binding_site ⇒ Object

  A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease.

• .nuclease_hypersensitive_site ⇒ Object

  -- No comment or description provided.

• .nuclease_sensitive_site ⇒ Object

  A region of nucleotide sequence targeted by a nuclease enzyme.

• .nucleic_acid ⇒ Object

  An attribute describing a sequence consisting of nucleobases bound to repeating units.

• .nucleomorph_gene ⇒ Object

  A gene from nucleomorph sequence.

• .nucleomorphic_chromosome ⇒ Object

  A chromosome originating in a nucleomorph.

• .nucleomorphic_sequence ⇒ Object

  -- No comment or description provided.

• .nucleotide_binding_site ⇒ Object

  A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues.

• .nucleotide_match ⇒ Object

  A match against a nucleotide sequence.

• .nucleotide_motif ⇒ Object

  A region of nucleotide sequence corresponding to a known motif.

• .nucleotide_to_protein_binding_site ⇒ Object

  A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.

• .octamer_motif ⇒ Object

  A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors.

• .Okazaki_fragment ⇒ Object

  Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication.

• .oligo ⇒ Object

  A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.

• .oligo_U_tail ⇒ Object

  The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602).

• .one_methyl_three_three_amino_three_carboxypropyl_pseudouridine ⇒ Object

  1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature.

• .one_methyladenosine ⇒ Object

  1_methyladenosine is a modified adenosine.

• .one_methylguanosine ⇒ Object

  1_methylguanosine is a modified guanosine base feature.

• .one_methylinosine ⇒ Object

  1-methylinosine is a modified insosine.

• .one_methylpseudouridine ⇒ Object

  1_methylpseudouridine is a modified uridine base feature.

• .one_two_prime_O_dimethyladenosine ⇒ Object

  1,2'-O-dimethyladenosine is a modified adenosine.

• .one_two_prime_O_dimethylguanosine ⇒ Object

  1_2prime_O_dimethylguanosine is a modified guanosine base feature.

• .one_two_prime_O_dimethylinosine ⇒ Object

  1,2'-O-dimethylinosine is a modified inosine.

• .open_chromatin_region ⇒ Object

  A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA.

• .operator ⇒ Object

  A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.

• .operon ⇒ Object

  A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region.

• .operon_member ⇒ Object

  -- No comment or description provided.

• .ORF ⇒ Object

  The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids.

• .organelle_sequence ⇒ Object

  -- No comment or description provided.

• .oriC ⇒ Object

  An origin of bacterial chromosome replication.

• .origin_of_replication ⇒ Object

  The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.

• .oriT ⇒ Object

  A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.

• .oriV ⇒ Object

  An origin of vegetative replication in plasmids and phages.

• .orphan ⇒ Object

  -- No comment or description provided.

• .orphan_CDS ⇒ Object

  A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence.

• .orthologous ⇒ Object

  An attribute describing a kind of homology where divergence occured after a speciation event.

• .orthologous_region ⇒ Object

  A homologous_region that is orthologous to another region.

• .orthologous_to ⇒ Object

  -- No comment or description provided.

• .outron ⇒ Object

  A region of a primary transcript, that is removed via trans splicing.

• .overlapping ⇒ Object

  An attribute describing a gene that has a sequence that overlaps the sequence of another gene.

• .overlapping_EST_set ⇒ Object

  A continous experimental result region extending the length of multiple overlapping EST's.

• .overlapping_feature_set ⇒ Object

  A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature.

• .overlaps ⇒ Object

  X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y.

• .OxyS_RNA ⇒ Object

  A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli.

• .p_element ⇒ Object

  A P_element is a DNA transposon responsible for hybrid dysgenesis.

• .PAC ⇒ Object

  The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage.

• .PAC_clone ⇒ Object

  -- No comment or description provided.

• .PAC_end ⇒ Object

  A region of sequence from the end of a PAC clone that may provide a highly specific marker.

• .paired_end_fragment ⇒ Object

  An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair).

• .paracentric ⇒ Object

  -- No comment or description provided.

• .paracentric_inversion ⇒ Object

  A chromosomal inversion that does not include the centromere.

• .parallel_beta_strand ⇒ Object

  A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal).

• .paralogous ⇒ Object

  An attribute describing a kind of homology where divergence occurred after a duplication event.

• .paralogous_region ⇒ Object

  A homologous_region that is paralogous to another region.

• .paralogous_to ⇒ Object

  -- No comment or description provided.

• .part_of ⇒ Object

  Either: Example: amino_acid part_of polypeptide.

• .partial_evidence_for_feature ⇒ Object

  B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.

• .partial_genomic_sequence_assembly ⇒ Object

  A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's.

• .partially_characterised_chromosomal_mutation ⇒ Object

  -- No comment or description provided.

• .partially_processed_cDNA_clone ⇒ Object

  A cDNA invalidated clone by partial processing.

• .paternal_uniparental_disomy ⇒ Object

  Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother.

• .paternal_variant ⇒ Object

  -- No comment or description provided.

• .paternally_imprinted ⇒ Object

  The paternal copy of the gene is modified, rendering it transcriptionally silent.

• .paternally_imprinted_gene ⇒ Object

  A gene that is paternally imprinted.

• .pathogenic_island ⇒ Object

  Mobile genetic elements that contribute to rapid changes in virulence potential.

• .PCB ⇒ Object

  A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle.

• .PCR_product ⇒ Object

  A region amplified by a PCR reaction.

• .pedigree_specific_variant ⇒ Object

  -- No comment or description provided.

• .peptide_coil ⇒ Object

  Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds).

• .peptide_collection ⇒ Object

  A collection of peptide sequences.

• .peptide_helix ⇒ Object

  A helix is a secondary_structure conformation where the peptide backbone forms a coil.

• .peptide_localization_signal ⇒ Object

  A region of peptide sequence used to target the polypeptide molecule to a specific organelle.

• .peptidyl ⇒ Object

  An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds.

• .pericentric ⇒ Object

  -- No comment or description provided.

• .pericentric_inversion ⇒ Object

  A chromosomal inversion that includes the centromere.

• .peroxywybutosine ⇒ Object

  Peroxywybutosine is a modified guanosine base feature.

• .Phage_RNA_Polymerase_Promoter ⇒ Object

  A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.

• .phage_sequence ⇒ Object

  The nucleotide sequence of a virus that infects bacteria.

• .phagemid ⇒ Object

  A plasmid which carries within its sequence a bacteriophage replication origin.

• .phagemid_clone ⇒ Object

  -- No comment or description provided.

• .phenylalanine ⇒ Object

  A place holder for a cross product with chebi.

• .phenylalanine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding phenylalanyl tRNA (SO:0000267).

• .phenylalanyl_tRNA ⇒ Object

  A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.

• .phosphorylation_site ⇒ Object

  A post-translationally modified region in which residues of the protein are modified by phosphorylation.

• .pi_helix ⇒ Object

  The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis.

• .PIP_box ⇒ Object

  A polypeptide region that mediates binding to PCNA.

• .piRNA ⇒ Object

  A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.

• .piRNA_gene ⇒ Object

  A gene that encodes for an piwi associated RNA.

• .plasmid ⇒ Object

  A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism.

• .plasmid_clone ⇒ Object

  -- No comment or description provided.

• .plasmid_gene ⇒ Object

  A gene from plasmid sequence.

• .plasmid_location ⇒ Object

  -- No comment or description provided.

• .plasmid_vector ⇒ Object

  -- No comment or description provided.

• .plastid_gene ⇒ Object

  A gene from plastid sequence.

• .plastid_sequence ⇒ Object

  -- No comment or description provided.

• .plus_1_frameshift ⇒ Object

  A frameshift caused by inserting one base.

• .plus_1_frameshift_variant ⇒ Object

  A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward.

• .plus_1_translational_frameshift ⇒ Object

  The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.

• .plus_1_translationally_frameshifted ⇒ Object

  An attribute describing a translational frameshift of +1.

• .plus_2_frameshift_variant ⇒ Object

  -- No comment or description provided.

• .plus_2_framshift ⇒ Object

  A frameshift caused by inserting two bases.

• .plus_2_translational_frameshift ⇒ Object

  The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.

• .PNA ⇒ Object

  An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds.

• .PNA_oligo ⇒ Object

  Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments.

• .point_centromere ⇒ Object

  A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S.

• .point_mutation ⇒ Object

  A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.

• .polinton ⇒ Object

  A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase.

• .polyA_primed_cDNA_clone ⇒ Object

  A cDNA clone invalidated by polyA priming.

• .polyA_sequence ⇒ Object

  Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.

• .polyA_signal_sequence ⇒ Object

  The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.

• .polyA_site ⇒ Object

  The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation.

• .polyadenylated ⇒ Object

  A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule.

• .polyadenylated_mRNA ⇒ Object

  An mRNA that is polyadenylated.

• .polyadenylation_variant ⇒ Object

  A sequence variant that changes polyadenylation with respect to a reference sequence.

• .polycistronic ⇒ Object

  An attribute describing a sequence that contains the code for more than one gene product.

• .polycistronic_gene ⇒ Object

  A gene that is polycistronic.

• .polycistronic_mRNA ⇒ Object

  An mRNA that encodes multiple proteins from at least two non-overlapping regions.

• .polycistronic_primary_transcript ⇒ Object

  A primary transcript encoding for more than one gene product.

• .polycistronic_transcript ⇒ Object

  A transcript that is polycistronic.

• .polymer_attribute ⇒ Object

  An attribute to describe the kind of biological sequence.

• .polymerase_synthesis_read ⇒ Object

  A read produced by the polymerase based sequence by synthesis method.

• .polymorphic_pseudogene ⇒ Object

  Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated.

• .polymorphic_sequence_variant ⇒ Object

  A sequence variant that is segregating in one or more natural populations of a species.

• .polymorphic_variant ⇒ Object

  -- No comment or description provided.

• .polypeptide ⇒ Object

  A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.

• .polypeptide_binding_motif ⇒ Object

  A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand.

• .polypeptide_calcium_ion_contact_site ⇒ Object

  A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions.

• .polypeptide_catalytic_motif ⇒ Object

  A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues.

• .polypeptide_cobalt_ion_contact_site ⇒ Object

  A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions.

• .polypeptide_conserved_motif ⇒ Object

  A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins.

• .polypeptide_conserved_region ⇒ Object

  A subsection of sequence with biological interest that is conserved in different proteins.

• .polypeptide_copper_ion_contact_site ⇒ Object

  A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions.

• .polypeptide_DNA_contact ⇒ Object

  A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA.

• .polypeptide_domain ⇒ Object

  A structurally or functionally defined protein region.

• .polypeptide_function_variant ⇒ Object

  A sequence variant which changes polypeptide functioning with respect to a reference sequence.

• .polypeptide_fusion ⇒ Object

  A sequence variant that causes a fusion of two polypeptide sequences.

• .polypeptide_gain_of_function_variant ⇒ Object

  A sequence variant which causes gain of polypeptide function with respect to a reference sequence.

• .polypeptide_iron_ion_contact_site ⇒ Object

  A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions.

• .polypeptide_ligand_contact ⇒ Object

  Residues which interact with a ligand.

• .polypeptide_localization_variant ⇒ Object

  A sequence variant which changes the localization of a polypeptide with respect to a reference sequence.

• .polypeptide_loss_of_function_variant ⇒ Object

  A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence.

• .polypeptide_magnesium_ion_contact_site ⇒ Object

  A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions.

• .polypeptide_manganese_ion_contact_site ⇒ Object

  A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions.

• .polypeptide_metal_contact ⇒ Object

  A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions.

• .polypeptide_molybdenum_ion_contact_site ⇒ Object

  A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions.

• .polypeptide_motif ⇒ Object

  A sequence motif is a short (up to 20 amino acids) region of biological interest.

• .polypeptide_nest_left_right_motif ⇒ Object

  A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.

• .polypeptide_nest_motif ⇒ Object

  A motif of two consecutive residues with dihedral angles.

• .polypeptide_nest_right_left_motif ⇒ Object

  A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.

• .polypeptide_nickel_ion_contact_site ⇒ Object

  A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions.

• .polypeptide_partial_loss_of_function ⇒ Object

  A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence.

• .polypeptide_post_translational_processing_affected ⇒ Object

  -- No comment or description provided.

• .polypeptide_post_translational_processing_variant ⇒ Object

  A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence.

• .polypeptide_region ⇒ Object

  Biological sequence region that can be assigned to a specific subsequence of a polypeptide.

• .polypeptide_repeat ⇒ Object

  A polypeptide_repeat is a single copy of an internal sequence repetition.

• .polypeptide_secondary_structure ⇒ Object

  A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain.

• .polypeptide_sequence_variant ⇒ Object

  A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence.

• .polypeptide_sequencing_information ⇒ Object

  Incompatibility in the sequence due to some experimental problem.

• .polypeptide_structural_motif ⇒ Object

  Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules.

• .polypeptide_structural_region ⇒ Object

  Region of polypeptide with a given structural property.

• .polypeptide_truncation ⇒ Object

  A sequence variant of the CD that causes a truncation of the resulting polypeptide.

• .polypeptide_tungsten_ion_contact_site ⇒ Object

  A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions.

• .polypeptide_turn_motif ⇒ Object

  A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues.

• .polypeptide_variation_site ⇒ Object

  A site of sequence variation (alteration).

• .polypeptide_zinc_ion_contact_site ⇒ Object

  A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions.

• .polyploid ⇒ Object

  A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number.

• .polypyrimidine_tract ⇒ Object

  The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.

• .population_specific_variant ⇒ Object

  -- No comment or description provided.

• .position_of ⇒ Object

  -- No comment or description provided.

• .positional_candidate_gene ⇒ Object

  A candidate gene whose association with a trait is based on the gene's location on a chromosome.

• .positive_sense_ssRNA_viral_sequence ⇒ Object

  A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host.

• .positively_autoregulated ⇒ Object

  The gene product is involved in its own transcriptional regulation, where it increases transcription.

• .positively_autoregulated_gene ⇒ Object

  A gene that is positively autoregulated.

• .possible_assembly_error ⇒ Object

  A region of sequence where there may have been an error in the assembly.

• .possible_base_call_error ⇒ Object

  A region of sequence where the validity of the base calling is questionable.

• .post_translationally_modified_region ⇒ Object

  A region where a transformation occurs in a protein after it has been synthesized.

• .post_translationally_regulated ⇒ Object

  An attribute describing a gene that is regulated after it has been translated.

• .post_translationally_regulated_by_protein_modification ⇒ Object

  An attribute describing a gene sequence where the resulting protein is modified to regulate it.

• .post_translationally_regulated_by_protein_stability ⇒ Object

  An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein.

• .post_translationally_regulated_gene ⇒ Object

  A gene that is post translationally regulated.

• .pre_edited_mRNA ⇒ Object

  -- No comment or description provided.

• .pre_edited_region ⇒ Object

  The region of a transcript that will be edited.

• .pre_miRNA ⇒ Object

  The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin sructure.

• .predicted ⇒ Object

  An attribute describing an unverified region.

• .predicted_ab_initio_computation ⇒ Object

  -- No comment or description provided.

• .predicted_by_ab_initio_computation ⇒ Object

  An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity.

• .predicted_gene ⇒ Object

  This term is mapped to MGED.

• .primary_transcript ⇒ Object

  A transcript that in its initial state requires modification to be functional.

• .primary_transcript_attribute ⇒ Object

  -- No comment or description provided.

• .primary_transcript_region ⇒ Object

  A part of a primary transcript.

• .primer ⇒ Object

  An oligo to which new deoxyribonucleotides can be added by DNA polymerase.

• .primer_binding_site ⇒ Object

  Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription.

• .primer_match ⇒ Object

  A nucleotide match to a primer sequence.

• .probe ⇒ Object

  A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid.

• .processed ⇒ Object

  An attribute describing a pseudogene where by an mRNA was retrotransposed.

• .processed_from ⇒ Object

  Inverse of processed_into.

• .processed_into ⇒ Object

  X is processed_into Y if a region X is modified to create Y.

• .processed_pseudogene ⇒ Object

  A pseudogene where by an mRNA was retrotransposed.

• .processed_transcript ⇒ Object

  A transcript for which no open reading frame has been identified and for which no other function has been determined.

• .processed_transcript_attribute ⇒ Object

  -- No comment or description provided.

• .proline ⇒ Object

  A place holder for a cross product with chebi.

• .proline_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding prolyl tRNA (SO:0000268).

• .prolyl_tRNA ⇒ Object

  A tRNA sequence that has a proline anticodon, and a 3' proline binding region.

• .promoter ⇒ Object

  A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.

• .promoter_element ⇒ Object

  -- No comment or description provided.

• .promoter_flanking_region ⇒ Object

  A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites.

• .promoter_region ⇒ Object

  A region of sequence which is part of a promoter.

• .promoter_targeting_sequence ⇒ Object

  A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter.

• .promoter_trap_construct ⇒ Object

  A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element.

• .propeptide ⇒ Object

  Part of a peptide chain which is cleaved off during the formation of the mature protein.

• .propeptide_cleavage_site ⇒ Object

  The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs.

• .prophage ⇒ Object

  A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated "island".

• .proplastid_gene ⇒ Object

  A gene from proplastid sequence.

• .proplastid_sequence ⇒ Object

  -- No comment or description provided.

• .protease_site ⇒ Object

  A polypeptide_region that codes for a protease cleavage site.

• .protein_altering_variant ⇒ Object

  A sequence_variant which is predicted to change the protein encoded in the coding sequence.

• .protein_binding_site ⇒ Object

  A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.

• .protein_coding ⇒ Object

  -- No comment or description provided.

• .protein_coding_gene ⇒ Object

  -- No comment or description provided.

• .protein_coding_primary_transcript ⇒ Object

  A primary transcript that, at least in part, encodes one or more proteins.

• .protein_hmm_match ⇒ Object

  A match to a protein HMM such as pfam.

• .protein_match ⇒ Object

  A match against a protein sequence.

• .protein_protein_contact ⇒ Object

  A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues.

• .protein_stability_element ⇒ Object

  A polypeptide region that proves structure in a protein that affects the stability of the protein.

• .proviral_gene ⇒ Object

  A gene from proviral sequence.

• .proviral_location ⇒ Object

  -- No comment or description provided.

• .proviral_region ⇒ Object

  A viral sequence which has integrated into a host genome.

• .proximal_promoter_element ⇒ Object

  DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor).

• .PSE_motif ⇒ Object

  A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III.

• .pseudogene ⇒ Object

  A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both).

• .pseudogene_attribute ⇒ Object

  An attribute of a pseudogene (SO:0000336).

• .pseudogene_by_unequal_crossing_over ⇒ Object

  A pseudogene caused by unequal crossing over at recombination.

• .pseudogenic_exon ⇒ Object

  A non functional descendant of an exon, part of a pseudogene.

• .pseudogenic_gene_segment ⇒ Object

  A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product.

• .pseudogenic_region ⇒ Object

  A non-functional descendent of a functional entity.

• .pseudogenic_rRNA ⇒ Object

  A non functional descendent of an rRNA.

• .pseudogenic_transcript ⇒ Object

  A non functional descendant of a transcript, part of a pseudogene.

• .pseudogenic_tRNA ⇒ Object

  A non functional descendent of a tRNA.

• .pseudoknot ⇒ Object

  A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop.

• .pseudouridine ⇒ Object

  A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position.

• .pseudouridylation_guide_snoRNA ⇒ Object

  A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.

• .purine_to_pyrimidine_transversion ⇒ Object

  Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T.

• .purine_transition ⇒ Object

  A substitution of a purine, A or G, for another purine.

• .pyrimidine_to_purine_transversion ⇒ Object

  Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G.

• .pyrimidine_transition ⇒ Object

  A substitution of a pyrimidine, C or T, for another pyrimidine.

• .pyrosequenced_read ⇒ Object

  A read produced by pyrosequencing technology.

• .pyrrolysine ⇒ Object

  A place holder for a cross product with chebi.

• .pyrrolysine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding pyrrolysyl tRNA (SO:0000766).

• .pyrrolysyl_tRNA ⇒ Object

  A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.

• .QTL ⇒ Object

  A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait.

• .quality_value ⇒ Object

  An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score.

• .quantitative_variant ⇒ Object

  -- No comment or description provided.

• .queuosine ⇒ Object

  Queuosine is a modified 7-deazoguanosine.

• .R_five_prime_LTR_region ⇒ Object

  -- No comment or description provided.

• .R_GNA ⇒ Object

  An attribute describing a GNA sequence in the (R)-GNA enantiomer.

• .R_GNA_oligo ⇒ Object

  An oligo composed of (R)-GNA residues.

• .R_LTR_region ⇒ Object

  -- No comment or description provided.

• .R_three_prime_LTR_region ⇒ Object

  -- No comment or description provided.

• .random_sequence ⇒ Object

  A sequence of nucleotides or amino acids which, by design, has a "random" order of components, given a predetermined input frequency of these components.

• .RAPD ⇒ Object

  RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers.

• .rare_variant ⇒ Object

  -- No comment or description provided.

• .rasiRNA ⇒ Object

  A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.

• .rate_of_transcription_variant ⇒ Object

  A sequence variant that changes the rate of transcription with respect to a reference sequence.

• .rDNA_intergenic_spacer_element ⇒ Object

  A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1).

• .rDNA_replication_fork_barrier ⇒ Object

  A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing.

• .read ⇒ Object

  A sequence obtained from a single sequencing experiment.

• .read_pair ⇒ Object

  One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.

• .reading_frame ⇒ Object

  A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids.

• .reagent ⇒ Object

  A sequence used in experiment.

• .reagent_attribute ⇒ Object

  Added jan 2006 by KE.

• .rearranged_at_DNA_level ⇒ Object

  An attribute to describe the sequence of a feature, where the DNA is rearranged.

• .rearrangement_breakpoint ⇒ Object

  A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization.

• .reciprocal ⇒ Object

  -- No comment or description provided.

• .reciprocal_chromosomal_translocation ⇒ Object

  A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged.

• .recoded ⇒ Object

  An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations.

• .recoded_by_translational_bypass ⇒ Object

  Recoded mRNA where a block of nucleotides is not translated.

• .recoded_codon ⇒ Object

  A codon that has been redefined at translation.

• .recoded_mRNA ⇒ Object

  The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals.

• .recoding_pseudoknot ⇒ Object

  The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding.

• .recoding_stimulatory_region ⇒ Object

  A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA.

• .recombination_feature ⇒ Object

  -- No comment or description provided.

• .recombination_feature_of_rearranged_gene ⇒ Object

  -- No comment or description provided.

• .recombination_hotspot ⇒ Object

  A region in a genome which promotes recombination.

• .recombination_regulatory_region ⇒ Object

  A regulatory region that is involved in the control of the process of recombination.

• .recombination_signal_sequence ⇒ Object

  A region recognized by a recombinase.

• .recombinationally_inverted_gene ⇒ Object

  A recombinationally rearranged gene by inversion.

• .recombinationally_rearranged ⇒ Object

  -- No comment or description provided.

• .recombinationally_rearranged_gene ⇒ Object

  A gene that is recombinationally rearranged.

• .recombinationally_rearranged_vertebrate_immune_system_gene ⇒ Object

  A recombinationally rearranged gene of the vertebrate immune system.

• .recombined_from ⇒ Object

  -- No comment or description provided.

• .recombined_to ⇒ Object

  -- No comment or description provided.

• .recursive_splice_site ⇒ Object

  A recursive splice site is a splice site which subdivides a large intron.

• .reference_genome ⇒ Object

  A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly.

• .region ⇒ Object

  A sequence_feature with an extent greater than zero.

• .regional_centromere ⇒ Object

  A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes.

• .regional_centromere_central_core ⇒ Object

  A conserved region within the central region of a modular centromere, where the kinetochore is formed.

• .regional_centromere_inner_repeat_region ⇒ Object

  The inner inverted repeat region of a modular centromere and part of the entral core surrounding a non-conserved central region.

• .regional_centromere_outer_repeat_region ⇒ Object

  The heterochromatic outer repeat region of a modular centromere.

• .regional_centromere_outer_repeat_transcript ⇒ Object

  A transcript that is transcribed from the outer repeat region of a regional centromere.

• .regulated ⇒ Object

  An attribute to describe a sequence that is regulated.

• .regulatory_promoter_element ⇒ Object

  A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region.

• .regulatory_region ⇒ Object

  A region of sequence that is involved in the control of a biological process.

• .regulatory_region_ablation ⇒ Object

  A feature ablation whereby the deleted region includes a regulatory region.

• .regulatory_region_amplification ⇒ Object

  A feature amplification of a region containing a regulatory region.

• .regulatory_region_fusion ⇒ Object

  A feature fusion where the deletion brings together regulatory regions.

• .regulatory_region_translocation ⇒ Object

  A feature translocation where the region contains a regulatory region.

• .regulatory_region_variant ⇒ Object

  A sequence variant located within a regulatory region.

• .regulon ⇒ Object

  A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal.

• .remark ⇒ Object

  A comment about the sequence.

• .repeat_component ⇒ Object

  A region of a repeated sequence.

• .repeat_family ⇒ Object

  A group of characterized repeat sequences.

• .repeat_fragment ⇒ Object

  A portion of a repeat, interrupted by the insertion of another element.

• .repeat_region ⇒ Object

  A region of sequence containing one or more repeat units.

• .repeat_unit ⇒ Object

  The simplest repeated component of a repeat region.

• .repetitive_element ⇒ Object

  -- No comment or description provided.

• .replication_regulatory_region ⇒ Object

  A regulatory region that is involved in the control of the process of nucleotide replication.

• .replicon ⇒ Object

  A region containing at least one unique origin of replication and a unique termination site.

• .rescue ⇒ Object

  An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype.

• .rescue_gene ⇒ Object

  A gene that rescues.

• .rescue_mini_gene ⇒ Object

  A mini_gene that rescues.

• .rescue_region ⇒ Object

  A region that rescues.

• .resolution_site ⇒ Object

  A region specifically recognised by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles.

• .restriction_enzyme_assembly_scar ⇒ Object

  A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends.

• .restriction_enzyme_binding_site ⇒ Object

  A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme.

• .restriction_enzyme_cleavage_junction ⇒ Object

  The boundary at which a restriction enzyme breaks the nucleotide sequence.

• .restriction_enzyme_cut_site ⇒ Object

  A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA.

• .restriction_enzyme_five_prime_single_strand_overhang ⇒ Object

  A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end.

• .restriction_enzyme_recognition_site ⇒ Object

  The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme.

• .restriction_enzyme_region ⇒ Object

  A region related to restriction enzyme function.

• .restriction_enzyme_single_strand_overhang ⇒ Object

  A terminal region of DNA sequence where the end of the region is not blunt ended.

• .restriction_enzyme_three_prime_single_strand_overhang ⇒ Object

  A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end.

• .restriction_fragment ⇒ Object

  A region of polynucleotide sequence produced by digestion with a restriction endonuclease.

• .retinoic_acid_responsive_element ⇒ Object

  A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind.

• .retrogene ⇒ Object

  -- No comment or description provided.

• .retron ⇒ Object

  Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes.

• .retrotransposed ⇒ Object

  An attribute of a feature that occurred as the product of a reverse transcriptase mediated event.

• .retrotransposon ⇒ Object

  A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase.

• .reverse ⇒ Object

  Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction.

• .reverse_Hoogsteen_base_pair ⇒ Object

  A type of non-canonical base-pairing.

• .reverse_primer ⇒ Object

  A single stranded oligo used for polymerase chain reaction.

• .RFLP_fragment ⇒ Object

  A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme.

• .RH_map ⇒ Object

  A radiation hybrid map is a physical map.

• .rho_dependent_bacterial_terminator ⇒ Object

  -- No comment or description provided.

• .rho_independent_bacterial_terminator ⇒ Object

  -- No comment or description provided.

• .ribonuclease_site ⇒ Object

  A region of a transcript encoding the cleavage site for a ribonuclease enzyme.

• .ribosome_entry_site ⇒ Object

  Region in mRNA where ribosome assembles.

• .riboswitch ⇒ Object

  A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression.

• .ribothymidine ⇒ Object

  A modified RNA base in which thymine is bound to the ribose ring.

• .ribozyme ⇒ Object

  An RNA with catalytic activity.

• .ribozymic ⇒ Object

  An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein.

• .right_handed_peptide_helix ⇒ Object

  A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw.

• .ring_chromosome ⇒ Object

  A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome.

• .RNA ⇒ Object

  An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone.

• .RNA_6S ⇒ Object

  A small (184-nt in E. coli) RNA that forms a hairpin type structure.

• .RNA_aptamer ⇒ Object

  RNA molecules that have been selected from random pools based on their ability to bind other molecules.

• .RNA_chromosome ⇒ Object

  Structural unit composed of a self-replicating, RNA molecule.

• .RNA_hook_turn ⇒ Object

  -- No comment or description provided.

• .RNA_internal_loop ⇒ Object

  A region of double stranded RNA where the bases do not conform to WC base pairing.

• .RNA_junction_loop ⇒ Object

  -- No comment or description provided.

• .RNA_motif ⇒ Object

  A motif that is active in RNA sequence.

• .RNA_polymerase_II_TATA_box ⇒ Object

  A TATA box core promoter of a gene transcribed by RNA polymerase II.

• .RNA_polymerase_III_TATA_box ⇒ Object

  A TATA box core promoter of a gene transcribed by RNA polymerase III.

• .RNA_polymerase_promoter ⇒ Object

  A region (DNA) to which RNA polymerase binds, to begin transcription.

• .RNA_replication_mode ⇒ Object

  This has been obsoleted as it represents a process.

• .RNA_sequence_secondary_structure ⇒ Object

  A folded RNA sequence.

• .RNA_stability_element ⇒ Object

  Either: RNA secondary structure that affects the stability of an RNA molecule.

• .RNAi_reagent ⇒ Object

  A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.

• .RNApol_I_promoter ⇒ Object

  A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription.

• .RNApol_II_core_promoter ⇒ Object

  The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.

• .RNApol_II_promoter ⇒ Object

  A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.

• .RNApol_II_promoter_region ⇒ Object

  A region of sequence which is a promoter for RNA polymerase II.

• .RNApol_III_promoter ⇒ Object

  A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription.

• .RNApol_III_promoter_type_1 ⇒ Object

  -- No comment or description provided.

• .RNApol_III_promoter_type_1_region ⇒ Object

  A region of sequence which is a promoter for RNA polymerase III type 1.

• .RNApol_III_promoter_type_2 ⇒ Object

  -- No comment or description provided.

• .RNApol_III_promoter_type_2_region ⇒ Object

  A region of sequence which is a promoter for RNA polymerase III type 2.

• .RNApol_III_promoter_type_3 ⇒ Object

  -- No comment or description provided.

• .RNase_MRP_RNA ⇒ Object

  The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes.

• .RNase_MRP_RNA_gene ⇒ Object

  A gene that encodes a RNase_MRP_RNA.

• .RNase_P_RNA ⇒ Object

  The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria.

• .RNase_P_RNA_gene ⇒ Object

  A gene that encodes an RNase P RNA.

• .Robertsonian_fusion ⇒ Object

  A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere.

• .rolling_circle ⇒ Object

  This has been obsoleted as it represents a process.

• .RprA_RNA ⇒ Object

  Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site.

• .RR_tract ⇒ Object

  A polypurine tract within an LTR_retrotransposon.

• .RRE_RNA ⇒ Object

  The Rev response element (RRE) is encoded within the HIV-env gene.

• .rRNA ⇒ Object

  RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.

• .rRNA_16S ⇒ Object

  A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome.

• .rRNA_18S ⇒ Object

  A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome.

• .rRNA_21S ⇒ Object

  A component of the large ribosomal subunit in mitochondrial rRNA.

• .rRNA_23S ⇒ Object

  A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome.

• .rRNA_25S ⇒ Object

  A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes.

• .rRNA_28S ⇒ Object

  A component of the large ribosomal subunit.

• .rRNA_5_8S ⇒ Object

  5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome.

• .rRNA_5S ⇒ Object

  5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes.

• .rRNA_cleavage_RNA ⇒ Object

  An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules.

• .rRNA_cleavage_snoRNA_primary_transcript ⇒ Object

  A primary transcript encoding an rRNA cleavage snoRNA.

• .rRNA_encoding ⇒ Object

  -- No comment or description provided.

• .rRNA_gene ⇒ Object

  A gene that encodes for ribosomal RNA.

• .rRNA_large_subunit_primary_transcript ⇒ Object

  A primary transcript encoding a large ribosomal subunit RNA.

• .rRNA_primary_transcript ⇒ Object

  A primary transcript encoding a ribosomal RNA.

• .rRNA_primary_transcript_region ⇒ Object

  A region of an rRNA primary transcript.

• .rRNA_small_subunit_primary_transcript ⇒ Object

  A primary transcript encoding a small ribosomal subunit RNA.

• .RST ⇒ Object

  A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long.

• .RST_match ⇒ Object

  A match against an RST sequence.

• .S_GNA ⇒ Object

  An attribute describing a GNA sequence in the (S)-GNA enantiomer.

• .S_GNA_oligo ⇒ Object

  An oligo composed of (S)-GNA residues.

• .S_region ⇒ Object

  The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell.

• .SAGE_tag ⇒ Object

  A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.

• .Sap1_recognition_motif ⇒ Object

  A DNA motif to which the S.

• .sarcin_like_RNA_motif ⇒ Object

  A loop in ribosomal RNA containing the sites of attack for ricin and sarcin.

• .satellite_DNA ⇒ Object

  The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.

• .schellmann_loop ⇒ Object

  A motif of six or seven consecutive residues that contains two H-bonds.

• .schellmann_loop_seven ⇒ Object

  Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5).

• .schellmann_loop_six ⇒ Object

  Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4).

• .score ⇒ Object

  The score of an experimentally derived feature such as a p-value.

• .scRNA ⇒ Object

  A small non coding RNA sequence, present in the cytoplasm.

• .scRNA_encoding ⇒ Object

  -- No comment or description provided.

• .scRNA_gene ⇒ Object

  -- No comment or description provided.

• .scRNA_primary_transcript ⇒ Object

  The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote.

• .SECIS_element ⇒ Object

  The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA.

• .selenocysteine ⇒ Object

  A place holder for a cross product with chebi.

• .selenocysteine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding seryl tRNA (SO:000269).

• .selenocysteinyl_tRNA ⇒ Object

  A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region.

• .sequence_alteration ⇒ Object

  A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.

• .sequence_assembly ⇒ Object

  A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.

• .sequence_attribute ⇒ Object

  An attribute describes a quality of sequence.

• .sequence_collection ⇒ Object

  A collection of discontinuous sequences.

• .sequence_conflict ⇒ Object

  Different sources report differing sequences.

• .sequence_difference ⇒ Object

  A region where the sequence differs from that of a specified sequence.

• .sequence_feature ⇒ Object

  Any extent of continuous biological sequence.

• .sequence_feature_locating_method ⇒ Object

  -- No comment or description provided.

• .sequence_length_variation ⇒ Object

  -- No comment or description provided.

• .sequence_location ⇒ Object

  -- No comment or description provided.

• .sequence_motif ⇒ Object

  A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.

• .sequence_of ⇒ Object

  -- No comment or description provided.

• .Sequence_Ontology ⇒ Object

  -- No comment or description provided.

• .sequence_operation ⇒ Object

  An operation that can be applied to a sequence, that results in a change.

• .sequence_rearrangement_feature ⇒ Object

  -- No comment or description provided.

• .sequence_replication_mode ⇒ Object

  This has been obsoleted as it represents a process.

• .sequence_secondary_structure ⇒ Object

  A folded sequence.

• .sequence_uncertainty ⇒ Object

  Describes the positions in a sequence where the authors are unsure about the sequence assignment.

• .sequence_variant ⇒ Object

  A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.

• .sequence_variant_affecting_3D_structure_of_polypeptide ⇒ Object

  A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule.

• .sequence_variant_affecting_copy_number ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_affecting_editing ⇒ Object

  Sequence variant affects the editing of the transcript.

• .sequence_variant_affecting_gene_structure ⇒ Object

  A sequence_variant_effect that changes the gene structure.

• .sequence_variant_affecting_level_of_translational_product ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_affecting_polyadenylation ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_affecting_polypeptide_amino_acid_sequence ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_affecting_polypeptide_function ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_affecting_rate_of_transcription ⇒ Object

  A mutation that alters the rate a which transcription of the sequence occurs.

• .sequence_variant_affecting_regulatory_region ⇒ Object

  A sequence_variant_effect which changes the regulatory region of a gene.

• .sequence_variant_affecting_splice_acceptor ⇒ Object

  A sequence_variant_effect that changes the splice acceptor sequence.

• .sequence_variant_affecting_splice_donor ⇒ Object

  A sequence_variant_effect that changes the splice donor sequence.

• .sequence_variant_affecting_splicing ⇒ Object

  A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed.

• .sequence_variant_affecting_transcript_processing ⇒ Object

  Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript.

• .sequence_variant_affecting_transcript_secondary_structure ⇒ Object

  A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule.

• .sequence_variant_affecting_transcript_stability ⇒ Object

  Sequence variant affects the stability of the transcript.

• .sequence_variant_affecting_transcription ⇒ Object

  Mutation affects the process of transcription, its initiation, progression or termination.

• .sequence_variant_affecting_translational_product ⇒ Object

  A sequence variant causing a change in primary translation product of a transcript.

• .sequence_variant_causes_exon_loss ⇒ Object

  A sequence variant affecting splicing and causes an exon loss.

• .sequence_variant_causes_intron_gain ⇒ Object

  A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072).

• .sequence_variant_causing_amino_acid_coding_codon_change_in_transcript ⇒ Object

  The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons.

• .sequence_variant_causing_amino_acid_deletion ⇒ Object

  The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence.

• .sequence_variant_causing_amino_acid_insertion ⇒ Object

  The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence.

• .sequence_variant_causing_amino_acid_substitution ⇒ Object

  The replacement of a single amino acid by another.

• .sequence_variant_causing_compensatory_transcript_secondary_structure_mutation ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_causing_complex_3D_structural_change ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_causing_complex_change_of_translational_product ⇒ Object

  Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms.

• .sequence_variant_causing_conformational_change ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_causing_conservative_amino_acid_substitution ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_causing_conservative_missense_codon_change_in_transcript ⇒ Object

  The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position.

• .sequence_variant_causing_cryptic_splice_acceptor_activation ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_causing_cryptic_splice_activation ⇒ Object

  A sequence variant causing a new (functional) splice site.

• .sequence_variant_causing_cryptic_splice_donor_activation ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_causing_gain_of_function_of_polypeptide ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_causing_gene_fusion ⇒ Object

  A sequence_variant_effect that changes the gene structure by causing a fusion to another gene.

• .sequence_variant_causing_inactive_catalytic_site ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_causing_inactive_ligand_binding_site ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_causing_initiator_codon_change_in_transcript ⇒ Object

  The DNA mutation changes, usually destroys, the first coding triplet of a gene.

• .sequence_variant_causing_loss_of_function_of_polypeptide ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_causing_minus_1_frameshift ⇒ Object

  A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide.

• .sequence_variant_causing_minus_2_frameshift ⇒ Object

  A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides.

• .sequence_variant_causing_missense_codon_change_in_transcript ⇒ Object

  The nucleotide change in the codon leads to a new codon coding for a new amino acid.

• .sequence_variant_causing_no_3D_structural_change ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_causing_no_change_in_transcript ⇒ Object

  No effect on the state of the RNA.

• .sequence_variant_causing_no_change_of_translational_product ⇒ Object

  The sequence variant at RNA level does not lead to any change in polypeptide.

• .sequence_variant_causing_non_synonymous_codon_change_in_transcript ⇒ Object

  A DNA point mutation that causes a substitution of an amino acid by an other.

• .sequence_variant_causing_nonconservative_amino_acid_substitution ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_causing_nonconservative_missense_codon_change_in_transcript ⇒ Object

  The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position.

• .sequence_variant_causing_nonsense_codon_change_in_transcript ⇒ Object

  The nucleotide change in the codon triplet creates a terminator codon.

• .sequence_variant_causing_partial_loss_of_function_of_polypeptide ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_causing_plus_1_frameshift_mutation ⇒ Object

  A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide.

• .sequence_variant_causing_plus_2_frameshift ⇒ Object

  A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides.

• .sequence_variant_causing_polypeptide_elongation ⇒ Object

  The extension of the translational product at either (or both) the N-terminus and/or the C-terminus.

• .sequence_variant_causing_polypeptide_fusion ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_causing_polypeptide_localization_change ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_causing_polypeptide_post_translational_processing_change ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_causing_polypeptide_truncation ⇒ Object

  The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062).

• .sequence_variant_causing_synonymous_codon_change_in_transcript ⇒ Object

  The changed codon has the same translation product as the original codon.

• .sequence_variant_causing_terminator_codon_change_in_transcript ⇒ Object

  The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence.

• .sequence_variant_decreasing_level_of_translation_product ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_decreasing_rate_of_transcription ⇒ Object

  A sequence variation that decreases the rate a which transcription of the sequence occurs.

• .sequence_variant_decreasing_transcript_stability ⇒ Object

  Sequence variant decreases the stability (half-life) of the transcript.

• .sequence_variant_effect ⇒ Object

  The effect of a change in nucleotide sequence.

• .sequence_variant_increasing_level_of_translation_product ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_increasing_rate_of_transcription ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variant_increasing_transcript_stability ⇒ Object

  Sequence variant increases the stability (half-life) of the transcript.

• .sequence_variant_obs ⇒ Object

  A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.

• .sequence_variation_affecting_coding_sequence ⇒ Object

  Any of the amino acid coding triplets of a gene are affected by the DNA mutation.

• .sequence_variation_affecting_level_of_transcript ⇒ Object

  A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.

• .sequence_variation_affecting_reading_frame ⇒ Object

  An umbrella term for terms describing an effect of a sequence variation on the frame of translation.

• .sequence_variation_affecting_transcript ⇒ Object

  Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence.

• .sequence_variation_affecting_transcript_sequence ⇒ Object

  OBSOLETE: This term was deleted as it conflated more than one term.

• .sequence_variation_decreasing_level_of_transcript ⇒ Object

  A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.

• .sequence_variation_increasing_level_of_transcript ⇒ Object

  A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.

• .sequencing_primer ⇒ Object

  -- No comment or description provided.

• .serine ⇒ Object

  A place holder for a cross product with chebi.

• .serine_threonine_motif ⇒ Object

  A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).

• .serine_threonine_staple_motif ⇒ Object

  A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative.

• .serine_threonine_turn ⇒ Object

  A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).

• .serine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding seryl tRNA (SO:000269).

• .seryl_tRNA ⇒ Object

  A tRNA sequence that has a serine anticodon, and a 3' serine binding region.

• .seven_aminomethyl_seven_deazaguanosine ⇒ Object

  7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine.

• .seven_cyano_seven_deazaguanosine ⇒ Object

  7_cyano_7_deazaguanosine is a modified 7-deazoguanosine.

• .seven_deazaguanosine ⇒ Object

  7-deazaguanosine is a moddified guanosine.

• .seven_methylguanine ⇒ Object

  A modified RNA base in which guanine is methylated at the 7- position.

• .seven_methylguanosine ⇒ Object

  7_methylguanosine is a modified guanosine base feature.

• .sgRNA ⇒ Object

  A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method.

• .shadow_enhancer ⇒ Object

  -- No comment or description provided.

• .Shine_Dalgarno_sequence ⇒ Object

  A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.

• .signal_anchor ⇒ Object

  A signal sequence that is not cleaved from the polypeptide.

• .signal_peptide ⇒ Object

  The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components.

• .signature ⇒ Object

  A region of sequence where developer information is encoded.

• .silenced ⇒ Object

  An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level.

• .silenced_by_DNA_methylation ⇒ Object

  An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription.

• .silenced_by_DNA_modification ⇒ Object

  An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription.

• .silenced_by_histone_deacetylation ⇒ Object

  An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation.

• .silenced_by_histone_methylation ⇒ Object

  An attribute describing an epigenetic process where a gene is inactivated by histone methylation.

• .silenced_by_histone_modification ⇒ Object

  An attribute describing an epigenetic process where a gene is inactivated by histone modification.

• .silenced_by_RNA_interference ⇒ Object

  An attribute describing an epigenetic process where a gene is inactivated by RNA interference.

• .silenced_gene ⇒ Object

  A gene that is silenced.

• .silencer ⇒ Object

  A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.

• .silent_mating_type_cassette_array ⇒ Object

  A gene cassette array that corresponds to a silenced version of a mating type region.

• .silent_mutation ⇒ Object

  A sequence variant that does not affect protein function.

• .similar_to ⇒ Object

  -- No comment or description provided.

• .simple_sequence_length_variation ⇒ Object

  -- No comment or description provided.

• .SINE_element ⇒ Object

  A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome.

• .single ⇒ Object

  Attributes added to describe the different kinds of replicon.

• .single_strand_restriction_enzyme_cleavage_site ⇒ Object

  A restriction enzyme cleavage site whereby only one strand is cut.

• .single_stranded_cDNA ⇒ Object

  -- No comment or description provided.

• .single_stranded_DNA_chromosome ⇒ Object

  Structural unit composed of a self-replicating, single-stranded DNA molecule.

• .single_stranded_RNA_chromosome ⇒ Object

  Structural unit composed of a self-replicating, single-stranded RNA molecule.

• .siRNA ⇒ Object

  A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA.

• .site ⇒ Object

  The interbase position where something (eg an aberration) occurred.

• .site_specific_recombination_target_region ⇒ Object

  -- No comment or description provided.

• .six_cutter_restriction_site ⇒ Object

  -- No comment or description provided.

• .SL10_acceptor_site ⇒ Object

  A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA.

• .SL11_acceptor_site ⇒ Object

  A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA.

• .SL12_acceptor_site ⇒ Object

  A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA.

• .SL1_acceptor_site ⇒ Object

  A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs.

• .SL2_acceptor_site ⇒ Object

  A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs.

• .SL3_acceptor_site ⇒ Object

  A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA.

• .SL4_acceptor_site ⇒ Object

  A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA.

• .SL5_acceptor_site ⇒ Object

  A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA.

• .SL6_acceptor_site ⇒ Object

  A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA.

• .SL7_acceptor_site ⇒ Object

  A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA.

• .SL8_acceptor_site ⇒ Object

  A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA.

• .SL9_acceptor_site ⇒ Object

  A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA.

• .small_regulatory_ncRNA ⇒ Object

  A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.

• .small_subunit_rRNA ⇒ Object

  Ribosomal RNA transcript that structures the small subunit of the ribosome.

• .smFISH_probe ⇒ Object

  A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment.

• .snoRNA ⇒ Object

  A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins.

• .snoRNA_encoding ⇒ Object

  -- No comment or description provided.

• .snoRNA_gene ⇒ Object

  -- No comment or description provided.

• .snoRNA_primary_transcript ⇒ Object

  A primary transcript encoding a small nucleolar mRNA (SO:0000275).

• .SNP ⇒ Object

  SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.

• .snRNA ⇒ Object

  A small nuclear RNA molecule involved in pre-mRNA splicing and processing.

• .snRNA_encoding ⇒ Object

  -- No comment or description provided.

• .snRNA_gene ⇒ Object

  -- No comment or description provided.

• .snRNA_primary_transcript ⇒ Object

  A primary transcript encoding a small nuclear RNA (SO:0000274).

• .SNV ⇒ Object

  SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.

• .solo_LTR ⇒ Object

  A recombination product between the 2 LTR of the same element.

• .somatic_variant ⇒ Object

  -- No comment or description provided.

• .sonicate_fragment ⇒ Object

  A DNA fragment generated by sonication.

• .SP6_RNA_Polymerase_Promoter ⇒ Object

  A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription.

• .specific_recombination_site ⇒ Object

  -- No comment or description provided.

• .splice_acceptor_variant ⇒ Object

  A splice variant that changes the 2 base region at the 3' end of an intron.

• .splice_donor_5th_base_variant ⇒ Object

  A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript.

• .splice_donor_variant ⇒ Object

  A splice variant that changes the 2 base pair region at the 5' end of an intron.

• .splice_enhancer ⇒ Object

  Region of a transcript that regulates splicing.

• .splice_junction ⇒ Object

  The boundary between an intron and an exon.

• .splice_region ⇒ Object

  A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.

• .splice_region_variant ⇒ Object

  A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.

• .splice_site ⇒ Object

  Consensus region of primary transcript bordering junction of splicing.

• .splice_site_variant ⇒ Object

  A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript.

• .spliced_leader_RNA ⇒ Object

  -- No comment or description provided.

• .spliceosomal_intron ⇒ Object

  An intron which is spliced by the spliceosome.

• .spliceosomal_intron_region ⇒ Object

  A region within an intron.

• .splicing_feature ⇒ Object

  -- No comment or description provided.

• .splicing_regulatory_region ⇒ Object

  A regulatory_region that modulates splicing.

• .splicing_variant ⇒ Object

  A sequence variant that changes the process of splicing.

• .spot_42_RNA ⇒ Object

  A 109-nucleotide RNA of E.

• .SRP_RNA ⇒ Object

  The signal recognition particle (SRP) is a universally conserved ribonucleoprotein.

• .SRP_RNA_encoding ⇒ Object

  -- No comment or description provided.

• .SRP_RNA_gene ⇒ Object

  -- No comment or description provided.

• .SRP_RNA_primary_transcript ⇒ Object

  A primary transcript encoding a signal recognition particle RNA.

• .ss_oligo ⇒ Object

  A single stranded oligonucleotide.

• .ss_RNA_viral_sequence ⇒ Object

  A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA.

• .st_turn_left_handed_type_one ⇒ Object

  The peptide twists in an anticlockwise, left handed manner.

• .st_turn_left_handed_type_two ⇒ Object

  The peptide twists in an anticlockwise, left handed manner.

• .st_turn_right_handed_type_one ⇒ Object

  The peptide twists in an clockwise, right handed manner.

• .st_turn_right_handed_type_two ⇒ Object

  The peptide twists in an clockwise, right handed manner.

• .standard_draft ⇒ Object

  The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs.

• .start_codon ⇒ Object

  First codon to be translated by a ribosome.

• .started_by ⇒ Object

  X is strted_by Y if Y is part_of X and X and Y share a 5' boundary.

• .starts ⇒ Object

  X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary.

• .status ⇒ Object

  An attribute describing the status of a feature, based on the available evidence.

• .status_of_coding_sequence ⇒ Object

  -- No comment or description provided.

• .stem_loop ⇒ Object

  A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences.

• .sterol_regulatory_element ⇒ Object

  A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism.

• .sticky_end_restriction_enzyme_cleavage_site ⇒ Object

  -- No comment or description provided.

• .stop_codon ⇒ Object

  In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.

• .stop_codon_read_through ⇒ Object

  A stop codon redefined to be a new amino acid.

• .stop_codon_readthrough ⇒ Object

  -- No comment or description provided.

• .stop_codon_redefined_as_pyrrolysine ⇒ Object

  A stop codon redefined to be the new amino acid, pyrrolysine.

• .stop_codon_redefined_as_selenocysteine ⇒ Object

  A stop codon redefined to be the new amino acid, selenocysteine.

• .stop_codon_redefinition_as_pyrrolysine ⇒ Object

  -- No comment or description provided.

• .stop_codon_redefinition_as_selenocysteine ⇒ Object

  -- No comment or description provided.

• .stop_codon_signal ⇒ Object

  A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding.

• .stop_gained ⇒ Object

  A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript.

• .stop_lost ⇒ Object

  A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript.

• .stop_retained_variant ⇒ Object

  A sequence variant where at least one base in the terminator codon is changed, but the terminator remains.

• .strand_attribute ⇒ Object

  Attributes added to describe the different kinds of replicon.

• .STREP_motif ⇒ Object

  A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2.

• .stRNA ⇒ Object

  Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C.

• .stRNA_encoding ⇒ Object

  -- No comment or description provided.

• .stRNA_gene ⇒ Object

  -- No comment or description provided.

• .stRNA_primary_transcript ⇒ Object

  A primary transcript encoding a small temporal mRNA (SO:0000649).

• .structural_alteration ⇒ Object

  -- No comment or description provided.

• .structural_variant ⇒ Object

  A sequence variant that changes one or more sequence features.

• .STS ⇒ Object

  Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known.

• .STS_map ⇒ Object

  An STS map is a physical map organized by the unique STS landmarks.

• .substitute ⇒ Object

  To substitute a subsection of sequence for another.

• .substitute_A_to_I ⇒ Object

  An edit to substitute an I for an A.

• .substitute_C_to_U ⇒ Object

  An edit to substitute an U for a C.

• .substitution ⇒ Object

  A sequence alteration where the length of the change in the variant is the same as that of the reference.

• .subtelomere ⇒ Object

  A heterochromatic region of the chromosome, adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed.

• .sugar_edge_base_pair ⇒ Object

  A type of non-canonical base-pairing.

• .supercontig ⇒ Object

  One or more contigs that have been ordered and oriented using end-read information.

• .supported_by_domain_match ⇒ Object

  An attribute to describe a feature that has been predicted using sequence similarity of a known domain.

• .supported_by_EST_or_cDNA ⇒ Object

  An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data.

• .supported_by_sequence_similarity ⇒ Object

  An attribute to describe a feature that has been predicted using sequence similarity techniques.

• .symbiosis_island ⇒ Object

  A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria.

• .symmetric_RNA_internal_loop ⇒ Object

  An internal RNA loop where the extent of the loop on both stands is the same size.

• .synonymous ⇒ Object

  -- No comment or description provided.

• .synonymous_variant ⇒ Object

  A sequence variant where there is no resulting change to the encoded amino acid.

• .syntenic ⇒ Object

  Attribute describing sequence regions occurring in same order on chromosome of different species.

• .syntenic_region ⇒ Object

  A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species.

• .synthetic_oligo ⇒ Object

  An oligo composed of synthetic nucleotides.

• .synthetic_sequence ⇒ Object

  An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence.

• .T3_RNA_Polymerase_Promoter ⇒ Object

  A DNA sequence to which the T3 RNA polymerase binds, to begin transcription.

• .T7_RNA_Polymerase_Promoter ⇒ Object

  A region (DNA) to which the T7 RNA polymerase binds, to begin transcription.

• .T_loop ⇒ Object

  Non-base-paired sequence of three nucleotide bases in tRNA.

• .T_to_A_transversion ⇒ Object

  A transversion from T to A.

• .T_to_C_transition ⇒ Object

  -- No comment or description provided.

• .T_to_G_transversion ⇒ Object

  A transversion from T to G.

• .tag ⇒ Object

  A nucleotide sequence that may be used to identify a larger sequence.

• .tandem ⇒ Object

  -- No comment or description provided.

• .tandem_duplication ⇒ Object

  A duplication consisting of 2 identical adjacent regions.

• .tandem_repeat ⇒ Object

  Two or more adjcent copies of a region (of length greater than 1).

• .target_site_duplication ⇒ Object

  A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion.

• .targeting_vector ⇒ Object

  An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications.

• .tasiRNA ⇒ Object

  The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene.

• .tasiRNA_primary_transcript ⇒ Object

  A primary transcript encoding a tasiRNA.

• .TATA_box ⇒ Object

  A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T).

• .TCT_motif ⇒ Object

  A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS.

• .telomerase_RNA ⇒ Object

  The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.

• .telomerase_RNA_gene ⇒ Object

  A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase.

• .telomere ⇒ Object

  A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.

• .telomeric_repeat ⇒ Object

  The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n.

• .telomeric_transcript ⇒ Object

  A non-coding transcript derived from thetranscript of the telomere.

• .template_region ⇒ Object

  A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA.

• .terminal_inverted_repeat ⇒ Object

  An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon.

• .terminal_inverted_repeat_element ⇒ Object

  A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long.

• .terminator ⇒ Object

  The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.

• .terminator_codon_variant ⇒ Object

  A sequence variant whereby at least one of the bases in the terminator codon is changed.

• .terminator_of_type_2_RNApol_III_promoter ⇒ Object

  A terminator signal for RNA polymerase III transcription.

• .TERRA ⇒ Object

  A non-coding RNA transcript, derived from the transcription of the telomere.

• .tetraloop ⇒ Object

  A base-paired stem with loop of 4 non-hydrogen bonded nucleotides.

• .tetranucleotide_repeat_microsatellite_feature ⇒ Object

  -- No comment or description provided.

• .TF_binding_site ⇒ Object

  A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667].

• .TF_binding_site_variant ⇒ Object

  A sequence variant located within a transcription factor binding site.

• .TFBS_ablation ⇒ Object

  A feature ablation whereby the deleted region includes a transcription factor binding site.

• .TFBS_amplification ⇒ Object

  A feature amplification of a region containing a transcription factor binding site.

• .TFBS_fusion ⇒ Object

  A fusion where the deletion brings together transcription factor binding sites.

• .TFBS_translocation ⇒ Object

  A feature translocation where the region contains a transcription factor binding site.

• .theta_replication ⇒ Object

  This has been obsoleted as it represents a process.

• .three_methylcytidine ⇒ Object

  3-methylcytidine is a modified cytidine.

• .three_methylpseudouridine ⇒ Object

  3_methylpseudouridine is a modified uridine base feature.

• .three_methyluridine ⇒ Object

  3_methyluridine is a modified uridine base feature.

• .three_prime_cis_splice_site ⇒ Object

  Intronic 2 bp region bordering the exon, at the 3' edge of the intron.

• .three_prime_clip ⇒ Object

  3'-most region of a precursor transcript that is clipped off during processing.

• .three_prime_coding_exon ⇒ Object

  The coding exon that is most 3-prime on a given transcript.

• .three_prime_coding_exon_coding_region ⇒ Object

  The sequence of the three_prime_coding_exon that codes for protein.

• .three_prime_coding_exon_noncoding_region ⇒ Object

  The sequence of the 3' exon that is not coding.

• .three_prime_D_heptamer ⇒ Object

  7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.

• .three_prime_D_nonamer ⇒ Object

  A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.

• .three_prime_D_recombination_signal_sequence ⇒ Object

  Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene.

• .three_prime_D_spacer ⇒ Object

  A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS.

• .three_prime_EST ⇒ Object

  An EST read from the 3' end of a transcript.

• .three_prime_five_prime_overlap ⇒ Object

  An attribute to describe a gene when the 3' region overlaps with another gene's 5' region.

• .three_prime_flanking_region ⇒ Object

  A flanking region located three prime of a specific region.

• .three_prime_intron ⇒ Object

  -- No comment or description provided.

• .three_prime_LTR ⇒ Object

  -- No comment or description provided.

• .three_prime_LTR_component ⇒ Object

  -- No comment or description provided.

• .three_prime_noncoding_exon ⇒ Object

  Non-coding exon in the 3' UTR.

• .three_prime_RACE_clone ⇒ Object

  A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host.

• .three_prime_recoding_site ⇒ Object

  The recoding stimulatory signal located downstream of the recoding site.

• .three_prime_repeat_recoding_signal ⇒ Object

  A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements.

• .three_prime_restriction_enzyme_junction ⇒ Object

  -- No comment or description provided.

• .three_prime_RST ⇒ Object

  A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long.

• .three_prime_stem_loop_structure ⇒ Object

  A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region.

• .three_prime_sticky_end_restriction_enzyme_cleavage_site ⇒ Object

  A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs.

• .three_prime_terminal_inverted_repeat ⇒ Object

  -- No comment or description provided.

• .three_prime_three_prime_overlap ⇒ Object

  An attribute to describe a gene when the 3' region overlaps with another gene's 3' region.

• .three_prime_UST ⇒ Object

  A UST located in the 3'UTR of a protein-coding transcript.

• .three_prime_UTR ⇒ Object

  A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.

• .three_prime_UTR_intron ⇒ Object

  An intron located in the 3' UTR.

• .three_ten_helix ⇒ Object

  The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis.

• .three_three_amino_three_carboxypropyl_uridine ⇒ Object

  3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature.

• .three_two_prime_O_dimethyluridine ⇒ Object

  3_2prime_O_dimethyluridine is a modified uridine base feature.

• .threonine ⇒ Object

  A place holder for a cross product with chebi.

• .threonine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding threonyl tRNA (SO:000270).

• .threonyl_tRNA ⇒ Object

  A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.

• .tiling_path ⇒ Object

  A set of regions which overlap with minimal polymorphism to form a linear sequence.

• .tiling_path_clone ⇒ Object

  A clone which is part of a tiling path.

• .tiling_path_fragment ⇒ Object

  A piece of sequence that makes up a tiling_path (SO:0000472).

• .tmRNA ⇒ Object

  A tmRNA liberates a mRNA from a stalled ribosome.

• .tmRNA_acceptor_piece ⇒ Object

  The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine.

• .tmRNA_coding_piece ⇒ Object

  The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag.

• .tmRNA_encoding ⇒ Object

  -- No comment or description provided.

• .tmRNA_gene ⇒ Object

  -- No comment or description provided.

• .tmRNA_primary_transcript ⇒ Object

  A primary transcript encoding a tmRNA (SO:0000584).

• .tmRNA_region ⇒ Object

  A region of a tmRNA.

• .TNA ⇒ Object

  An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone.

• .TNA_oligo ⇒ Object

  An oligo composed of TNA residues.

• .topologically_defined_region ⇒ Object

  A region that is defined according to its relations with other regions within the same sequence.

• .topology_attribute ⇒ Object

  Attributes added to describe the different kinds of replicon.

• .TR_box ⇒ Object

  A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S.

• .trans_splice_acceptor_site ⇒ Object

  The 3' splice site of the acceptor primary transcript.

• .trans_splice_donor_site ⇒ Object

  The 5' five prime splice site region of the donor RNA.

• .trans_splice_junction ⇒ Object

  The boundary between the spliced leader and the first exon of the mRNA.

• .trans_splice_site ⇒ Object

  Primary transcript region bordering trans-splice junction.

• .trans_spliced ⇒ Object

  An attribute describing transcript sequence that is created by splicing exons from diferent genes.

• .trans_spliced_from ⇒ Object

  -- No comment or description provided.

• .trans_spliced_mRNA ⇒ Object

  An mRNA that is trans-spliced.

• .trans_spliced_to ⇒ Object

  -- No comment or description provided.

• .trans_spliced_transcript ⇒ Object

  A transcript that is trans-spliced.

• .transcribed_cluster ⇒ Object

  A region defined by a set of transcribed sequences from the same gene or expressed pseudogene.

• .transcribed_fragment ⇒ Object

  An experimental region, defined by a tiling array experiment to be transcribed at some level.

• .transcribed_from ⇒ Object

  X is transcribed_from Y if X is synthesized from template Y.

• .transcribed_region ⇒ Object

  A region of sequence that is transcribed.

• .transcribed_spacer_region ⇒ Object

  Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA.

• .transcribed_to ⇒ Object

  Inverse of transcribed_from.

• .transcript ⇒ Object

  An RNA synthesized on a DNA or RNA template by an RNA polymerase.

• .transcript_ablation ⇒ Object

  A feature ablation whereby the deleted region includes a transcript feature.

• .transcript_amplification ⇒ Object

  A feature amplification of a region containing a transcript.

• .transcript_attribute ⇒ Object

  -- No comment or description provided.

• .transcript_bound_by_nucleic_acid ⇒ Object

  A transcript that is bound by a nucleic acid.

• .transcript_bound_by_protein ⇒ Object

  A transcript that is bound by a protein.

• .transcript_edited_by_U_insertion_deletion ⇒ Object

  The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.

• .transcript_feature ⇒ Object

  -- No comment or description provided.

• .transcript_function_variant ⇒ Object

  A sequence variant which alters the functioning of a transcript with respect to a reference sequence.

• .transcript_fusion ⇒ Object

  A feature fusion where the deletion brings together transcript regions.

• .transcript_processing_variant ⇒ Object

  A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence.

• .transcript_region ⇒ Object

  A region of a transcript.

• .transcript_regulatory_region_fusion ⇒ Object

  A feature fusion where the deletion brings together a regulatory region and a transcript region.

• .transcript_secondary_structure_variant ⇒ Object

  A sequence variant within a transcript that changes the secondary structure of the RNA product.

• .transcript_sequence_variant ⇒ Object

  -- No comment or description provided.

• .transcript_stability_variant ⇒ Object

  A variant that changes the stability of a transcript with respect to a reference sequence.

• .transcript_translocation ⇒ Object

  A feature translocation where the region contains a transcript.

• .transcript_variant ⇒ Object

  A sequence variant that changes the structure of the transcript.

• .transcript_with_readthrough_stop_codon ⇒ Object

  -- No comment or description provided.

• .transcript_with_translational_frameshift ⇒ Object

  A transcript with a translational frameshift.

• .transcription_end_site ⇒ Object

  The base where transcription ends.

• .transcription_regulatory_region ⇒ Object

  A regulatory region that is involved in the control of the process of transcription.

• .transcription_start_cluster ⇒ Object

  A region defined by a cluster of experimentally determined transcription starting sites.

• .transcription_variant ⇒ Object

  A variant that changes alters the transcription of a transcript with respect to a reference sequence.

• .transcriptional_cis_regulatory_region ⇒ Object

  A regulatory_region that modulates the transcription of a gene or genes.

• .transcriptionally_constitutive ⇒ Object

  Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate.

• .transcriptionally_induced ⇒ Object

  An inducer molecule is required for transcription to occur.

• .transcriptionally_regulated ⇒ Object

  An attribute describing a gene that is regulated at transcription.

• .transcriptionally_repressed ⇒ Object

  A repressor molecule is required for transcription to stop.

• .transgene ⇒ Object

  A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another.

• .transgene_attribute ⇒ Object

  -- No comment or description provided.

• .transgenic ⇒ Object

  Attribute describing sequence that has been integrated with foreign sequence.

• .transgenic_insertion ⇒ Object

  An insertion that derives from another organism, via the use of recombinant DNA technology.

• .transgenic_transposable_element ⇒ Object

  TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE.

• .transit_peptide ⇒ Object

  The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle).

• .transition ⇒ Object

  Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide.

• .translated_nucleotide_match ⇒ Object

  A match against a translated sequence.

• .translates_to ⇒ Object

  Inverse of translation _of.

• .translation_of ⇒ Object

  X is translation of Y if Y is translated by ribosome to create X.

• .translation_regulatory_region ⇒ Object

  A regulatory region that is involved in the control of the process of translation.

• .translational_frameshift ⇒ Object

  The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.

• .translational_product_function_variant ⇒ Object

  A sequence variant that affects the functioning of a translational product with respect to a reference sequence.

• .translational_product_level_variant ⇒ Object

  A functional variant that changes the translational product level with respect to a reference sequence.

• .translational_product_structure_variant ⇒ Object

  A sequence variant within the transcript that changes the structure of the translational product.

• .translationally_frameshifted ⇒ Object

  Recoding by frameshifting a particular site.

• .translationally_regulated ⇒ Object

  An attribute describing a gene that is regulated as it is translated.

• .translationally_regulated_gene ⇒ Object

  A gene that is translationally regulated.

• .translocate ⇒ Object

  To translocate a subsection of sequence.

• .translocation ⇒ Object

  A region of nucleotide sequence that has translocated to a new position.

• .translocation_breakpoint ⇒ Object

  The point within a chromosome where a translocation begins or ends.

• .translocation_element ⇒ Object

  A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently.

• .translocaton_attribute ⇒ Object

  -- No comment or description provided.

• .transmembrane_helix ⇒ Object

  A region that traverses the lipid bilayer and adopts a helical secondary structure.

• .transmembrane_polypeptide_region ⇒ Object

  Polypeptide region traversing the lipid bilayer.

• .transposable_element ⇒ Object

  A transposon or insertion sequence.

• .transposable_element_attribute ⇒ Object

  Added by KE Jan 2006 to capture the kinds of attributes of TEs (http://purl.obolibrary.org/obo/SO_0000780).

• .transposable_element_CDS ⇒ Object

  A CDS that is part of a transposable element.

• .transposable_element_flanking_region ⇒ Object

  The region of sequence surrounding a transposable element.

• .transposable_element_gene ⇒ Object

  A gene encoded within a transposable element.

• .transposable_element_insertion_site ⇒ Object

  The junction in a genome where a transposable_element has inserted.

• .transposable_element_pseudogene ⇒ Object

  A pseudogene contained within a transposable element.

• .transposon_fragment ⇒ Object

  A portion of a transposon, interrupted by the insertion of another element.

• .transversion ⇒ Object

  Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa.

• .trinucleotide_repeat_microsatellite_feature ⇒ Object

  -- No comment or description provided.

• .tRNA ⇒ Object

  Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length.

• .tRNA_encoding ⇒ Object

  -- No comment or description provided.

• .tRNA_gene ⇒ Object

  -- No comment or description provided.

• .tRNA_intron ⇒ Object

  An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification.

• .tRNA_primary_transcript ⇒ Object

  A primary transcript encoding a transfer RNA (SO:0000253).

• .tRNA_region ⇒ Object

  A region of a tRNA.

• .tryptophan ⇒ Object

  A place holder for a cross product with chebi.

• .tryptophan_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding tryptophanyl tRNA (SO:000271).

• .tryptophanyl_tRNA ⇒ Object

  A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.

• .TSS ⇒ Object

  The first base where RNA polymerase begins to synthesize the RNA transcript.

• .TSS_region ⇒ Object

  The region of a gene from the 5' most TSS to the 3' TSS.

• .twintron ⇒ Object

  An intron within an intron.

• .two_methyladenosine ⇒ Object

  2_methyladenosine is a modified adenosine.

• .two_methylthio_N6_cis_hydroxyisopentenyl_adenosine ⇒ Object

  2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.

• .two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine ⇒ Object

  2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine.

• .two_methylthio_N6_isopentenyladenosine ⇒ Object

  2_methylthio_N6_isopentenyladenosine is a modified adenosine.

• .two_methylthio_N6_methyladenosine ⇒ Object

  2_methylthio_N6_methyladenosine is a modified adenosine.

• .two_methylthio_N6_threonyl_carbamoyladenosine ⇒ Object

  2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine.

• .two_prime_O_methyladenosine ⇒ Object

  2prime_O_methyladenosine is a modified adenosine.

• .two_prime_O_methylcytidine ⇒ Object

  2'-O-methylcytidine is a modified cytidine.

• .two_prime_O_methylguanosine ⇒ Object

  2prime_O_methylguanosine is a modified guanosine base feature.

• .two_prime_O_methylinosine ⇒ Object

  2'-O-methylinosine is a modified inosine.

• .two_prime_O_methylpseudouridine ⇒ Object

  2prime_O_methylpseudouridine is a modified uridine base feature.

• .two_prime_O_methyluridine ⇒ Object

  2prime_O_methyluridine is a modified uridine base feature.

• .two_prime_O_ribosyladenosine_phosphate ⇒ Object

  2prime_O_ribosyladenosine_phosphate is a modified adenosine.

• .two_prime_O_ribosylguanosine_phosphate ⇒ Object

  2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature.

• .two_thio_two_prime_O_methyluridine ⇒ Object

  2_thio_2prime_O_methyluridine is a modified uridine base feature.

• .two_thiocytidine ⇒ Object

  2-thiocytidine is a modified cytidine.

• .two_thiouridine ⇒ Object

  2_thiouridine is a modified uridine base feature.

• .type_I_enzyme_restriction_site ⇒ Object

  The recognition site is bipartite and interrupted.

• .type_II_enzyme_restriction_site ⇒ Object

  The recognition site is either palindromic, partially palindromic or an interrupted palindrome.

• .tyrosine ⇒ Object

  A place holder for a cross product with chebi.

• .tyrosine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding tyrosyl tRNA (SO:000272).

• .tyrosyl_tRNA ⇒ Object

  A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.

• .U11_snRNA ⇒ Object

  U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.

• .U12_intron ⇒ Object

  A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.

• .U12_snRNA ⇒ Object

  The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.

• .U14_snoRNA ⇒ Object

  U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs.

• .U14_snoRNA_primary_transcript ⇒ Object

  The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.

• .U1_snRNA ⇒ Object

  U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing).

• .U2_intron ⇒ Object

  A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs.

• .U2_snRNA ⇒ Object

  U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing).

• .U3_five_prime_LTR_region ⇒ Object

  -- No comment or description provided.

• .U3_LTR_region ⇒ Object

  -- No comment or description provided.

• .U3_snoRNA ⇒ Object

  U3 snoRNA is a member of the box C/D class of small nucleolar RNAs.

• .U3_three_prime_LTR_region ⇒ Object

  -- No comment or description provided.

• .U4_snRNA ⇒ Object

  U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome.

• .U4atac_snRNA ⇒ Object

  An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns.

• .U5_five_prime_LTR_region ⇒ Object

  -- No comment or description provided.

• .U5_LTR_region ⇒ Object

  -- No comment or description provided.

• .U5_snRNA ⇒ Object

  U5 RNA is a component of both types of known spliceosome.

• .U5_three_prime_LTR_region ⇒ Object

  -- No comment or description provided.

• .U6_snRNA ⇒ Object

  U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA.

• .U6atac_snRNA ⇒ Object

  U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns.

• .U_box ⇒ Object

  An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription.

• .UAA_stop_codon_signal ⇒ Object

  A stop codon signal for a UAA stop codon redefinition.

• .UAG_stop_codon_signal ⇒ Object

  A stop codon signal for a UAG stop codon redefinition.

• .UGA_stop_codon_signal ⇒ Object

  A stop codon signal for a UGA stop codon redefinition.

• .ultracontig ⇒ Object

  An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.

• .unassigned_supercontig ⇒ Object

  A supercontig that is not been assigned to any ultracontig during a genome assembly project.

• .uncharacterised_chromosomal_mutation ⇒ Object

  -- No comment or description provided.

• .undermodified_hydroxywybutosine ⇒ Object

  Undermodified_hydroxywybutosine is a modified guanosine base feature.

• .unedited_region ⇒ Object

  The region of an edited transcript that will not be edited.

• .unequally_crossed_over ⇒ Object

  An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination.

• .unigene_cluster ⇒ Object

  A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene.

• .uninverted_insertional_duplication ⇒ Object

  An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.

• .uninverted_interchromosomal_transposition ⇒ Object

  An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.

• .uninverted_intrachromosomal_transposition ⇒ Object

  An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.

• .unique_variant ⇒ Object

  A physical quality which inheres to the variant by virtue of the number instances of the variant within a population.

• .unitary_pseudogene ⇒ Object

  A pseudogene, deactivated from original state by mutation, fixed in a population.

• .unoriented_insertional_duplication ⇒ Object

  An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.

• .unoriented_interchromosomal_transposition ⇒ Object

  An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.

• .unoriented_intrachromosomal_transposition ⇒ Object

  An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.

• .untranslated_region_polycistronic_mRNA ⇒ Object

  The untranslated sequence separating the 'cistrons' of multicistronic mRNA.

• .UPD ⇒ Object

  Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent.

• .upstream_AUG_codon ⇒ Object

  A start codon upstream of the ORF.

• .upstream_gene_variant ⇒ Object

  A sequence variant located 5' of a gene.

• .upstream_transcript_variant ⇒ Object

  A feature variant, where the alteration occurs upstream of the transcript TSS.

• .uridine_five_oxyacetic_acid ⇒ Object

  Uridine_5_oxyacetic_acid is a modified uridine base feature.

• .uridine_five_oxyacetic_acid_methyl_ester ⇒ Object

  Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature.

• .UST ⇒ Object

  An EST spanning part or all of the untranslated regions of a protein-coding transcript.

• .UST_match ⇒ Object

  A match against an UST sequence.

• .UTR ⇒ Object

  Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.

• .UTR_intron ⇒ Object

  Intron located in the untranslated region.

• .UTR_region ⇒ Object

  A region of UTR.

• .UTR_variant ⇒ Object

  A transcript variant that is located within the UTR.

• .V_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene.

• .V_D_DJ_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene.

• .V_D_DJ_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene.

• .V_D_DJ_J_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene.

• .V_D_DJ_J_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene.

• .V_D_J_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene.

• .V_D_J_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene.

• .V_DJ_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene.

• .V_DJ_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene.

• .V_DJ_J_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene.

• .V_DJ_J_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene.

• .V_gene_recombination_feature ⇒ Object

  Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene.

• .V_gene_segment ⇒ Object

  Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR.

• .V_heptamer ⇒ Object

  7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.

• .V_J_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene.

• .V_J_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene.

• .V_nonamer ⇒ Object

  9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.

• .V_region ⇒ Object

  The variable region of an immunoglobulin polypeptide sequence.

• .V_spacer ⇒ Object

  12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene.

• .V_VDJ_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene.

• .V_VDJ_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene.

• .V_VDJ_J_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene.

• .V_VDJ_J_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene.

• .V_VJ_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene.

• .V_VJ_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene.

• .V_VJ_J_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene.

• .V_VJ_J_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene.

• .vacuolar_sorting_signal ⇒ Object

  A polypeptide region that targets a polypeptide to the vacuole.

• .validated ⇒ Object

  An attribute to describe a feature that has been proven.

• .validated_cDNA_clone ⇒ Object

  A cDNA clone that has been validated.

• .valine ⇒ Object

  A place holder for a cross product with chebi.

• .valine_tRNA_primary_transcript ⇒ Object

  A primary transcript encoding valyl tRNA (SO:000273).

• .valyl_tRNA ⇒ Object

  A tRNA sequence that has a valine anticodon, and a 3' valine binding region.

• .variant_collection ⇒ Object

  A collection of one or more sequences of an individual.

• .variant_frequency ⇒ Object

  A physical quality which inheres to the variant by virtue of the number instances of the variant within a population.

• .variant_genome ⇒ Object

  A collection of sequences (often chromosomes) of an individual.

• .variant_of ⇒ Object

  Either: A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.

• .variant_origin ⇒ Object

  A quality inhering in a variant by virtue of its origin.

• .variant_phenotype ⇒ Object

  A quality inhering in a variant by virtue of its phenotype.

• .variant_quality ⇒ Object

  A dependent entity that inheres in a bearer, a sequence variant.

• .vault_RNA ⇒ Object

  A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex.

• .VD_gene_segment ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205).

• .VDJ_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene.

• .VDJ_gene_segment ⇒ Object

  Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).

• .VDJ_J_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene.

• .VDJ_J_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene.

• .vector_replicon ⇒ Object

  A replicon that has been modified to act as a vector for foreign sequence.

• .vertebrate_immune_system_feature ⇒ Object

  -- No comment or description provided.

• .vertebrate_immune_system_gene_recombination_feature ⇒ Object

  -- No comment or description provided.

• .vertebrate_immune_system_gene_recombination_signal_feature ⇒ Object

  -- No comment or description provided.

• .vertebrate_immune_system_gene_recombination_spacer ⇒ Object

  -- No comment or description provided.

• .vertebrate_immunoglobulin_T_cell_receptor_gene_cluster ⇒ Object

  -- No comment or description provided.

• .vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster ⇒ Object

  -- No comment or description provided.

• .vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment ⇒ Object

  -- No comment or description provided.

• .vertebrate_immunoglobulin_T_cell_receptor_segment ⇒ Object

  I am using the term segment instead of gene here to avoid confusion with the region 'gene'.

• .viral_sequence ⇒ Object

  The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell.

• .virtual_sequence ⇒ Object

  A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database.

• .VJ_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene.

• .VJ_gene_segment ⇒ Object

  Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).

• .VJ_J_C_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene.

• .VJ_J_cluster ⇒ Object

  Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene.

• .W_region ⇒ Object

  The leftmost segment of homology in the HML and MAT mating loci, but not present in HMR.

• .WC_base_pair ⇒ Object

  The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation.

• .whole_genome_sequence_status ⇒ Object

  The status of whole genome sequence.

• .wild_type ⇒ Object

  An attribute describing sequence with the genotype found in nature and/or standard laboratory stock.

• .wild_type_rescue_gene ⇒ Object

  A gene that rescues.

• .with_parent(uris, parent) ⇒ Object

  Returns only those URIs that fall under a designated parent URI.

• .wobble_base_pair ⇒ Object

  A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs.

• .wybutosine ⇒ Object

  Wybutosine is a modified guanosine base feature.

• .wyosine ⇒ Object

  Wyosine is a modified guanosine base feature.

• .X_element ⇒ Object

  The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site.

• .X_element_combinatorial_repeat ⇒ Object

  An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element.

• .Y_prime_element ⇒ Object

  A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies.

• .Y_region ⇒ Object

  A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha).

• .Y_RNA ⇒ Object

  Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins.

• .YAC ⇒ Object

  Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells.

• .YAC_clone ⇒ Object

  -- No comment or description provided.

• .YAC_end ⇒ Object

  A region of sequence from the end of a YAC clone that may provide a highly specific marker.

• .Z1_region ⇒ Object

  A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR).

• .Z2_region ⇒ Object

  A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR).

• .zinc_finger_binding_site ⇒ Object

  -- No comment or description provided.

• .zinc_repressed_element ⇒ Object

  A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc.

Class Method Details

.a_2KB_upstream_variant ⇒ Object

A sequence variant located within 2KB 5' of a gene. (http://purl.obolibrary.org/obo/SO_0001636)

# File 'lib/biointerchange/so.rb', line 10051

def self.a_2KB_upstream_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001636')
end

.a_3_prime_UTR_variant ⇒ Object

A UTR variant of the 3' UTR. (http://purl.obolibrary.org/obo/SO_0001624)

# File 'lib/biointerchange/so.rb', line 9985

def self.a_3_prime_UTR_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001624')
end

.a_3D_polypeptide_structure_variant ⇒ Object

A sequence variant that changes the resulting polypeptide structure. (http://purl.obolibrary.org/obo/SO_0001599)

# File 'lib/biointerchange/so.rb', line 9835

def self.a_3D_polypeptide_structure_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001599')
end

.a_4_methylcytosine ⇒ Object

A cytosine methylated at the 4 nitrogen. (http://purl.obolibrary.org/obo/SO_0001919)

# File 'lib/biointerchange/so.rb', line 11719

def self.a_4_methylcytosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001919')
end

.a_500B_downstream_variant ⇒ Object

A sequence variant located within a half KB of the end of a gene. (http://purl.obolibrary.org/obo/SO_0001634)

# File 'lib/biointerchange/so.rb', line 10039

def self.a_500B_downstream_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001634')
end

.a_5_carboxylcytosine ⇒ Object

A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon. (http://purl.obolibrary.org/obo/SO_0001966)

# File 'lib/biointerchange/so.rb', line 12005

def self.a_5_carboxylcytosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001966')
end

.a_5_formylcytosine ⇒ Object

A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon. (http://purl.obolibrary.org/obo/SO_0001961)

# File 'lib/biointerchange/so.rb', line 11975

def self.a_5_formylcytosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001961')
end

.a_5_hydroxymethylcytosine ⇒ Object

A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon. (http://purl.obolibrary.org/obo/SO_0001960)

# File 'lib/biointerchange/so.rb', line 11969

def self.a_5_hydroxymethylcytosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001960')
end

.a_5_methylcytosine ⇒ Object

A cytosine methylated at the 5 carbon. (http://purl.obolibrary.org/obo/SO_0001918)

# File 'lib/biointerchange/so.rb', line 11713

def self.a_5_methylcytosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001918')
end

.a_5_prime_UTR_premature_start_codon_gain_variant ⇒ Object

A 5' UTR variant where a premature start codon is gained. (http://purl.obolibrary.org/obo/SO_0001988)

# File 'lib/biointerchange/so.rb', line 12131

def self.a_5_prime_UTR_premature_start_codon_gain_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001988')
end

.a_5_prime_UTR_premature_start_codon_loss_variant ⇒ Object

A 5' UTR variant where a premature start codon is lost. (http://purl.obolibrary.org/obo/SO_0001989)

# File 'lib/biointerchange/so.rb', line 12137

def self.a_5_prime_UTR_premature_start_codon_loss_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001989')
end

.a_5_prime_UTR_premature_start_codon_variant ⇒ Object

A 5' UTR variant where a premature start codon is introduced, moved or lost. (http://purl.obolibrary.org/obo/SO_0001983)

# File 'lib/biointerchange/so.rb', line 12101

def self.a_5_prime_UTR_premature_start_codon_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001983')
end

.a_5_prime_UTR_variant ⇒ Object

A UTR variant of the 5' UTR. (http://purl.obolibrary.org/obo/SO_0001623)

# File 'lib/biointerchange/so.rb', line 9979

def self.a_5_prime_UTR_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001623')
end

.a_5KB_downstream_variant ⇒ Object

A sequence variant located within 5 KB of the end of a gene. (http://purl.obolibrary.org/obo/SO_0001633)

# File 'lib/biointerchange/so.rb', line 10033

def self.a_5KB_downstream_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001633')
end

.a_5KB_upstream_variant ⇒ Object

A sequence variant located within 5KB 5' of a gene. (http://purl.obolibrary.org/obo/SO_0001635)

# File 'lib/biointerchange/so.rb', line 10045

def self.a_5KB_upstream_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001635')
end

.a_8_oxoadenine ⇒ Object

A modified DNA adenine base,at the 8 carbon, often the product of DNA damage. (http://purl.obolibrary.org/obo/SO_0001967)

# File 'lib/biointerchange/so.rb', line 12011

def self.a_8_oxoadenine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001967')
end

.a_8_oxoguanine ⇒ Object

A modified DNA guanine base,at the 8 carbon, often the product of DNA damage. (http://purl.obolibrary.org/obo/SO_0001965)

# File 'lib/biointerchange/so.rb', line 11999

def self.a_8_oxoguanine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001965')
end

.A_box ⇒ Object

A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG. (http://purl.obolibrary.org/obo/SO_0000619)

# File 'lib/biointerchange/so.rb', line 4037

def self.A_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000619')
end

.A_box_type_1 ⇒ Object

An A box within an RNA polymerase III type 1 promoter. (http://purl.obolibrary.org/obo/SO_0001675)

# File 'lib/biointerchange/so.rb', line 10261

def self.A_box_type_1
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001675')
end

.A_box_type_2 ⇒ Object

An A box within an RNA polymerase III type 2 promoter. (http://purl.obolibrary.org/obo/SO_0001676)

# File 'lib/biointerchange/so.rb', line 10267

def self.A_box_type_2
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001676')
end

.A_minor_RNA_motif ⇒ Object

A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix. (http://purl.obolibrary.org/obo/SO_0000022)

# File 'lib/biointerchange/so.rb', line 441

def self.A_minor_RNA_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000022')
end

.A_to_C_transversion ⇒ Object

A transversion from adenine to cytidine. (http://purl.obolibrary.org/obo/SO_1000024)

# File 'lib/biointerchange/so.rb', line 12587

def self.A_to_C_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000024')
end

.A_to_G_transition ⇒ Object

A transition of an adenine to a guanine. (http://purl.obolibrary.org/obo/SO_1000015)

# File 'lib/biointerchange/so.rb', line 12533

def self.A_to_G_transition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000015')
end

.A_to_T_transversion ⇒ Object

A transversion from adenine to thymine. (http://purl.obolibrary.org/obo/SO_1000025)

# File 'lib/biointerchange/so.rb', line 12593

def self.A_to_T_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000025')
end

.AACCCT_box ⇒ Object

A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site. (http://purl.obolibrary.org/obo/SO_0001901)

# File 'lib/biointerchange/so.rb', line 11611

def self.AACCCT_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001901')
end

.aberrant_processed_transcript ⇒ Object

A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons. (SO:ke) (http://purl.obolibrary.org/obo/SO_0000681)

# File 'lib/biointerchange/so.rb', line 4409

def self.aberrant_processed_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000681')
end

.Ace2_UAS ⇒ Object

A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2. (http://purl.obolibrary.org/obo/SO_0001857)

# File 'lib/biointerchange/so.rb', line 11347

def self.Ace2_UAS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001857')
end

.active_peptide ⇒ Object

Active peptides are proteins which are biologically active, released from a precursor molecule. (http://purl.obolibrary.org/obo/SO_0001064)

# File 'lib/biointerchange/so.rb', line 6667

def self.active_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001064')
end

.adaptive_island ⇒ Object

An adaptive island is a genomic island that provides an adaptive advantage to the host. (http://purl.obolibrary.org/obo/SO_0000775)

# File 'lib/biointerchange/so.rb', line 4967

def self.adaptive_island
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000775')
end

.adjacent_to ⇒ Object

A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap. (http://purl.obolibrary.org/obo/so_2_5_2.obo#adjacent_to)

# File 'lib/biointerchange/so.rb', line 17

def self.adjacent_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#adjacent_to')
end

.AFLP_fragment ⇒ Object

A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments. (http://purl.obolibrary.org/obo/SO_0001830)

# File 'lib/biointerchange/so.rb', line 11185

def self.AFLP_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001830')
end

.alanine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001435)

# File 'lib/biointerchange/so.rb', line 8869

def self.alanine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001435')
end

.alanine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding alanyl tRNA. (http://purl.obolibrary.org/obo/SO_0000211)

# File 'lib/biointerchange/so.rb', line 1587

def self.alanine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000211')
end

.alanyl_tRNA ⇒ Object

A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region. (http://purl.obolibrary.org/obo/SO_0000254)

# File 'lib/biointerchange/so.rb', line 1845

def self.alanyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000254')
end

.allele ⇒ Object

An allele is one of a set of coexisting sequence variants of a gene. (http://purl.obolibrary.org/obo/SO_0001023)

# File 'lib/biointerchange/so.rb', line 6413

def self.allele
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001023')
end

.allelically_excluded ⇒ Object

Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell. (http://purl.obolibrary.org/obo/SO_0000137)

# File 'lib/biointerchange/so.rb', line 1139

def self.allelically_excluded
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000137')
end

.allelically_excluded_gene ⇒ Object

A gene that is allelically_excluded. (http://purl.obolibrary.org/obo/SO_0000897)

# File 'lib/biointerchange/so.rb', line 5663

def self.allelically_excluded_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000897')
end

.allopolyploid ⇒ Object

A polyploid where the multiple chromosome set was derived from a different organism. (http://purl.obolibrary.org/obo/SO_0001256)

# File 'lib/biointerchange/so.rb', line 7801

def self.allopolyploid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001256')
end

.alpha_beta_motif ⇒ Object

A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative. (http://purl.obolibrary.org/obo/SO_0100008)

# File 'lib/biointerchange/so.rb', line 12395

def self.alpha_beta_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100008')
end

.alpha_helix ⇒ Object

The helix has 3.6 residues per turn which corersponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier. (http://purl.obolibrary.org/obo/SO_0001117)

# File 'lib/biointerchange/so.rb', line 6973

def self.alpha_helix
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001117')
end

.alteration_attribute ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001508)

# File 'lib/biointerchange/so.rb', line 9307

def self.alteration_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001508')
end

.alternate_sequence_site ⇒ Object

Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. (http://purl.obolibrary.org/obo/SO_0001149)

# File 'lib/biointerchange/so.rb', line 7165

def self.alternate_sequence_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001149')
end

.alternately_spliced_gene_encodeing_one_transcript ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000503)

# File 'lib/biointerchange/so.rb', line 3337

def self.alternately_spliced_gene_encodeing_one_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000503')
end

.alternately_spliced_gene_encoding_greater_than_one_transcript ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000543)

# File 'lib/biointerchange/so.rb', line 3577

def self.alternately_spliced_gene_encoding_greater_than_one_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000543')
end

.alternatively_spliced ⇒ Object

An attribute describing a situation where a gene may encode for more than 1 transcript. (http://purl.obolibrary.org/obo/SO_0000877)

# File 'lib/biointerchange/so.rb', line 5543

def self.alternatively_spliced
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000877')
end

.alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_1001194)

# File 'lib/biointerchange/so.rb', line 13427

def self.alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001194')
end

.alternatively_spliced_transcript ⇒ Object

A transcript that is alternatively spliced. (http://purl.obolibrary.org/obo/SO_1001187)

# File 'lib/biointerchange/so.rb', line 13385

def self.alternatively_spliced_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001187')
end

.alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_1001244)

# File 'lib/biointerchange/so.rb', line 13457

def self.alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001244')
end

.ambisense_ssRNA_viral_sequence ⇒ Object

A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity. (http://purl.obolibrary.org/obo/SO_0001202)

# File 'lib/biointerchange/so.rb', line 7483

def self.ambisense_ssRNA_viral_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001202')
end

.amino_acid ⇒ Object

A sequence feature that corresponds to a single amino acid residue in a polypeptide. (http://purl.obolibrary.org/obo/SO_0001237)

# File 'lib/biointerchange/so.rb', line 7693

def self.amino_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001237')
end

.amino_acid_deletion ⇒ Object

A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide. (http://purl.obolibrary.org/obo/SO_0001604)

# File 'lib/biointerchange/so.rb', line 9865

def self.amino_acid_deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001604')
end

.amino_acid_insertion ⇒ Object

A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide. (http://purl.obolibrary.org/obo/SO_0001605)

# File 'lib/biointerchange/so.rb', line 9871

def self.amino_acid_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001605')
end

.amino_acid_substitution ⇒ Object

A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide. (http://purl.obolibrary.org/obo/SO_0001606)

# File 'lib/biointerchange/so.rb', line 9877

def self.amino_acid_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001606')
end

.amplification_origin ⇒ Object

An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence. (http://purl.obolibrary.org/obo/SO_0000750)

# File 'lib/biointerchange/so.rb', line 4823

def self.amplification_origin
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000750')
end

.anchor_binding_site ⇒ Object

Part of an edited transcript only. (http://purl.obolibrary.org/obo/SO_0000977)

# File 'lib/biointerchange/so.rb', line 6137

def self.anchor_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000977')
end

.anchor_region ⇒ Object

A region of a guide_RNA that base-pairs to a target mRNA. (http://purl.obolibrary.org/obo/SO_0000931)

# File 'lib/biointerchange/so.rb', line 5867

def self.anchor_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000931')
end

.androgen_response_element ⇒ Object

A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen. (http://purl.obolibrary.org/obo/SO_0001853)

# File 'lib/biointerchange/so.rb', line 11323

def self.androgen_response_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001853')
end

.aneuploid ⇒ Object

A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. (http://purl.obolibrary.org/obo/SO_0000054)

# File 'lib/biointerchange/so.rb', line 637

def self.aneuploid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000054')
end

.aneuploid_chromosome ⇒ Object

A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking. (http://purl.obolibrary.org/obo/SO_0000550)

# File 'lib/biointerchange/so.rb', line 3619

def self.aneuploid_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000550')
end

.annotation_directed_improved_draft ⇒ Object

The status of a whole genome sequence,where annotation, and verification of coding regions has occurred. (http://purl.obolibrary.org/obo/SO_0001489)

# File 'lib/biointerchange/so.rb', line 9193

def self.annotation_directed_improved_draft
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001489')
end

.anti_ARRET ⇒ Object

A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts are antisense of ARRET transcripts. (http://purl.obolibrary.org/obo/SO_0001926)

# File 'lib/biointerchange/so.rb', line 11761

def self.anti_ARRET
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001926')
end

.anticodon ⇒ Object

A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA. (http://purl.obolibrary.org/obo/SO_0001174)

# File 'lib/biointerchange/so.rb', line 7315

def self.anticodon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001174')
end

.anticodon_loop ⇒ Object

A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3. (http://purl.obolibrary.org/obo/SO_0001173)

# File 'lib/biointerchange/so.rb', line 7309

def self.anticodon_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001173')
end

.antiparallel_beta_strand ⇒ Object

A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets. (http://purl.obolibrary.org/obo/SO_0001112)

# File 'lib/biointerchange/so.rb', line 6943

def self.antiparallel_beta_strand
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001112')
end

.antisense ⇒ Object

A region sequence that is complementary to a sequence of messenger RNA. (http://purl.obolibrary.org/obo/SO_0000077)

# File 'lib/biointerchange/so.rb', line 779

def self.antisense
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000077')
end

.antisense_lncRNA ⇒ Object

Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA. (http://purl.obolibrary.org/obo/SO_0001904)

# File 'lib/biointerchange/so.rb', line 11629

def self.antisense_lncRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001904')
end

.antisense_primary_transcript ⇒ Object

The reverse complement of the primary transcript. (http://purl.obolibrary.org/obo/SO_0000645)

# File 'lib/biointerchange/so.rb', line 4193

def self.antisense_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000645')
end

.antisense_RNA ⇒ Object

Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA. (http://purl.obolibrary.org/obo/SO_0000644)

# File 'lib/biointerchange/so.rb', line 4187

def self.antisense_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000644')
end

.AP_1_binding_site ⇒ Object

A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors. (http://purl.obolibrary.org/obo/SO_0001842)

# File 'lib/biointerchange/so.rb', line 11257

def self.AP_1_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001842')
end

.apicoplast_chromosome ⇒ Object

A chromosome originating in an apicoplast. (http://purl.obolibrary.org/obo/SO_0001259)

# File 'lib/biointerchange/so.rb', line 7819

def self.apicoplast_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001259')
end

.apicoplast_gene ⇒ Object

A gene from apicoplast sequence. (http://purl.obolibrary.org/obo/SO_0000091)

# File 'lib/biointerchange/so.rb', line 863

def self.apicoplast_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000091')
end

.apicoplast_sequence ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000743)

# File 'lib/biointerchange/so.rb', line 4781

def self.apicoplast_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000743')
end

.aptamer ⇒ Object

DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. (http://purl.obolibrary.org/obo/SO_0000031)

# File 'lib/biointerchange/so.rb', line 495

def self.aptamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000031')
end

.archaeal_intron ⇒ Object

An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease. (http://purl.obolibrary.org/obo/SO_1001271)

# File 'lib/biointerchange/so.rb', line 13571

def self.archaeal_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001271')
end

.archaeosine ⇒ Object

Archaeosine is a modified 7-deazoguanosine. (http://purl.obolibrary.org/obo/SO_0001323)

# File 'lib/biointerchange/so.rb', line 8203

def self.archaeosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001323')
end

.arginine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001451)

# File 'lib/biointerchange/so.rb', line 8965

def self.arginine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001451')
end

.arginine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding arginyl tRNA (SO:0000255). (http://purl.obolibrary.org/obo/SO_0000212)

# File 'lib/biointerchange/so.rb', line 1593

def self.arginine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000212')
end

.arginyl_tRNA ⇒ Object

A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region. (http://purl.obolibrary.org/obo/SO_0001036)

# File 'lib/biointerchange/so.rb', line 6491

def self.arginyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001036')
end

.ARIA ⇒ Object

A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts consist of C rich repeats. (http://purl.obolibrary.org/obo/SO_0001925)

# File 'lib/biointerchange/so.rb', line 11755

def self.ARIA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001925')
end

.ARRET ⇒ Object

A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats. (http://purl.obolibrary.org/obo/SO_0001924)

# File 'lib/biointerchange/so.rb', line 11749

def self.ARRET
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001924')
end

.ARS ⇒ Object

A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host. (http://purl.obolibrary.org/obo/SO_0000436)

# File 'lib/biointerchange/so.rb', line 2931

def self.ARS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000436')
end

.ARS_consensus_sequence ⇒ Object

The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS. (http://purl.obolibrary.org/obo/SO_0002004)

# File 'lib/biointerchange/so.rb', line 12227

def self.ARS_consensus_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002004')
end

.asparagine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001449)

# File 'lib/biointerchange/so.rb', line 8953

def self.asparagine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001449')
end

.asparagine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding asparaginyl tRNA (SO:0000256). (http://purl.obolibrary.org/obo/SO_0000213)

# File 'lib/biointerchange/so.rb', line 1599

def self.asparagine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000213')
end

.asparaginyl_tRNA ⇒ Object

A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region. (http://purl.obolibrary.org/obo/SO_0000256)

# File 'lib/biointerchange/so.rb', line 1857

def self.asparaginyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000256')
end

.aspartic_acid ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001453)

# File 'lib/biointerchange/so.rb', line 8977

def self.aspartic_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001453')
end

.aspartic_acid_tRNA_primary_transcript ⇒ Object

A primary transcript encoding aspartyl tRNA (SO:0000257). (http://purl.obolibrary.org/obo/SO_0000214)

# File 'lib/biointerchange/so.rb', line 1605

def self.aspartic_acid_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000214')
end

.aspartyl_tRNA ⇒ Object

A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region. (http://purl.obolibrary.org/obo/SO_0000257)

# File 'lib/biointerchange/so.rb', line 1863

def self.aspartyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000257')
end

.ASPE_primer ⇒ Object

"A primer containing an SNV at the 3' end for accurate genotyping. (http://www.ncbi.nlm.nih.gov/pubmed/11252801) (http://purl.obolibrary.org/obo/SO_0001698)

# File 'lib/biointerchange/so.rb', line 10399

def self.ASPE_primer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001698')
end

.assembly ⇒ Object

A region of the genome of known length that is composed by ordering and aligning two or more different regions. (http://purl.obolibrary.org/obo/SO_0001248)

# File 'lib/biointerchange/so.rb', line 7753

def self.assembly
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001248')
end

.assembly_component ⇒ Object

A region of known length which may be used to manufacture a longer region. (http://purl.obolibrary.org/obo/SO_0000143)

# File 'lib/biointerchange/so.rb', line 1175

def self.assembly_component
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000143')
end

.assembly_error_correction ⇒ Object

A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake. (http://purl.obolibrary.org/obo/SO_0001525)

# File 'lib/biointerchange/so.rb', line 9409

def self.assembly_error_correction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001525')
end

.associated_with ⇒ Object

This relationship is vague and up for discussion. (http://purl.obolibrary.org/obo/so_2_5_2.obo#associated_with)

# File 'lib/biointerchange/so.rb', line 23

def self.associated_with
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#associated_with')
end

.assortment_derived_aneuploid ⇒ Object

Either:

-- No comment or description provided. --
(http://purl.obolibrary.org/obo/SO_0000058)

Or:

A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication.
(http://purl.obolibrary.org/obo/SO_0000803)

# File 'lib/biointerchange/so.rb', line 665

def self.assortment_derived_aneuploid
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000058'), RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000803') ]
end

.assortment_derived_deficiency ⇒ Object

Either:

-- No comment or description provided. --
(http://purl.obolibrary.org/obo/SO_0000052)

Or:

A multi-chromosome deficiency aberration generated by reassortment of other aberration components.
(http://purl.obolibrary.org/obo/SO_0000802)

# File 'lib/biointerchange/so.rb', line 625

def self.assortment_derived_deficiency
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000052'), RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000802') ]
end

.assortment_derived_deficiency_plus_duplication ⇒ Object

Either:

-- No comment or description provided. --
(http://purl.obolibrary.org/obo/SO_0000554)

Or:

A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication.
(http://purl.obolibrary.org/obo/SO_0000801)

# File 'lib/biointerchange/so.rb', line 3647

def self.assortment_derived_deficiency_plus_duplication
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000554'), RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000801') ]
end

.assortment_derived_duplication ⇒ Object

Either:

-- No comment or description provided. --
(http://purl.obolibrary.org/obo/SO_0000437)

Or:

A multi-chromosome duplication aberration generated by reassortment of other aberration components.
(http://purl.obolibrary.org/obo/SO_0000800)

# File 'lib/biointerchange/so.rb', line 2941

def self.assortment_derived_duplication
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000437'), RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000800') ]
end

.assortment_derived_variation ⇒ Object

A chromosome variation derived from an event during meiosis. (http://purl.obolibrary.org/obo/SO_0001504)

# File 'lib/biointerchange/so.rb', line 9283

def self.assortment_derived_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001504')
end

.asx_motif ⇒ Object

A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4). (http://purl.obolibrary.org/obo/SO_0001106)

# File 'lib/biointerchange/so.rb', line 6907

def self.asx_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001106')
end

.asx_turn ⇒ Object

A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2). (http://purl.obolibrary.org/obo/SO_0000912)

# File 'lib/biointerchange/so.rb', line 5753

def self.asx_turn
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000912')
end

.asx_turn_left_handed_type_one ⇒ Object

Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. (http://purl.obolibrary.org/obo/SO_0001129)

# File 'lib/biointerchange/so.rb', line 7045

def self.asx_turn_left_handed_type_one
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001129')
end

.asx_turn_left_handed_type_two ⇒ Object

Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. (http://purl.obolibrary.org/obo/SO_0001130)

# File 'lib/biointerchange/so.rb', line 7051

def self.asx_turn_left_handed_type_two
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001130')
end

.asx_turn_right_handed_type_one ⇒ Object

Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. (http://purl.obolibrary.org/obo/SO_0001132)

# File 'lib/biointerchange/so.rb', line 7063

def self.asx_turn_right_handed_type_one
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001132')
end

.asx_turn_right_handed_type_two ⇒ Object

Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. (http://purl.obolibrary.org/obo/SO_0001131)

# File 'lib/biointerchange/so.rb', line 7057

def self.asx_turn_right_handed_type_two
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001131')
end

.asymmetric_RNA_internal_loop ⇒ Object

An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand. (http://purl.obolibrary.org/obo/SO_0000021)

# File 'lib/biointerchange/so.rb', line 435

def self.asymmetric_RNA_internal_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000021')
end

.attB_site ⇒ Object

An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site. (http://purl.obolibrary.org/obo/SO_0000943)

# File 'lib/biointerchange/so.rb', line 5939

def self.attB_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000943')
end

.attC_site ⇒ Object

An attC site is a sequence required for the integration of a DNA of an integron. (http://purl.obolibrary.org/obo/SO_0000950)

# File 'lib/biointerchange/so.rb', line 5981

def self.attC_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000950')
end

.attCtn_site ⇒ Object

An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon. (http://purl.obolibrary.org/obo/SO_0001043)

# File 'lib/biointerchange/so.rb', line 6533

def self.attCtn_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001043')
end

.attenuator ⇒ Object

A sequence segment located within the five prime end of an mRNA that causes premature termination of translation. (http://purl.obolibrary.org/obo/SO_0000140)

# File 'lib/biointerchange/so.rb', line 1157

def self.attenuator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000140')
end

.attI_site ⇒ Object

A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place. (http://purl.obolibrary.org/obo/SO_0000367)

# File 'lib/biointerchange/so.rb', line 2517

def self.attI_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000367')
end

.attL_site ⇒ Object

A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site. (http://purl.obolibrary.org/obo/SO_0000944)

# File 'lib/biointerchange/so.rb', line 5945

def self.attL_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000944')
end

.attP_site ⇒ Object

An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome. (http://purl.obolibrary.org/obo/SO_0000942)

# File 'lib/biointerchange/so.rb', line 5933

def self.attP_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000942')
end

.attR_site ⇒ Object

A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site. (http://purl.obolibrary.org/obo/SO_0000945)

# File 'lib/biointerchange/so.rb', line 5951

def self.attR_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000945')
end

.AU_rich_element ⇒ Object

A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable. (http://purl.obolibrary.org/obo/SO_0001180)

# File 'lib/biointerchange/so.rb', line 7351

def self.AU_rich_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001180')
end

.autocatalytically_spliced_intron ⇒ Object

A self spliced intron. (http://purl.obolibrary.org/obo/SO_0000588)

# File 'lib/biointerchange/so.rb', line 3851

def self.autocatalytically_spliced_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000588')
end

.autopolyploid ⇒ Object

A polyploid where the multiple chromosome set was derived from the same organism. (http://purl.obolibrary.org/obo/SO_0001255)

# File 'lib/biointerchange/so.rb', line 7795

def self.autopolyploid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001255')
end

.autoregulated ⇒ Object

The gene product is involved in its own transcriptional regulation. (http://purl.obolibrary.org/obo/SO_0000471)

# File 'lib/biointerchange/so.rb', line 3145

def self.autoregulated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000471')
end

.autosynaptic_chromosome ⇒ Object

An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome. (http://purl.obolibrary.org/obo/SO_1000136)

# File 'lib/biointerchange/so.rb', line 13163

def self.autosynaptic_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000136')
end

.B_box ⇒ Object

A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC. (http://purl.obolibrary.org/obo/SO_0000620)

# File 'lib/biointerchange/so.rb', line 4043

def self.B_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000620')
end

.BAC ⇒ Object

Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host. (http://purl.obolibrary.org/obo/SO_0000153)

# File 'lib/biointerchange/so.rb', line 1235

def self.BAC
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000153')
end

.BAC_clone ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000764)

# File 'lib/biointerchange/so.rb', line 4907

def self.BAC_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000764')
end

.BAC_cloned_genomic_insert ⇒ Object

Requested by Andy Schroder - Flybase Harvard, Nov 2006. (http://purl.obolibrary.org/obo/SO_0000992)

# File 'lib/biointerchange/so.rb', line 6227

def self.BAC_cloned_genomic_insert
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000992')
end

.BAC_end ⇒ Object

A region of sequence from the end of a BAC clone that may provide a highly specific marker. (http://purl.obolibrary.org/obo/SO_0000999)

# File 'lib/biointerchange/so.rb', line 6269

def self.BAC_end
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000999')
end

.BAC_read_contig ⇒ Object

A contig of BAC reads. (http://purl.obolibrary.org/obo/SO_0001866)

# File 'lib/biointerchange/so.rb', line 11401

def self.BAC_read_contig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001866')
end

.bacterial_RNApol_promoter ⇒ Object

A DNA sequence to which bacterial RNA polymerase binds, to begin transcription. (http://purl.obolibrary.org/obo/SO_0000613)

# File 'lib/biointerchange/so.rb', line 4001

def self.bacterial_RNApol_promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000613')
end

.bacterial_RNApol_promoter_region ⇒ Object

A region which is part of a bacterial RNA polymerase promoter. (http://purl.obolibrary.org/obo/SO_0000843)

# File 'lib/biointerchange/so.rb', line 5339

def self.bacterial_RNApol_promoter_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000843')
end

.bacterial_RNApol_promoter_sigma54 ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001672)

# File 'lib/biointerchange/so.rb', line 10243

def self.bacterial_RNApol_promoter_sigma54
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001672')
end

.bacterial_RNApol_promoter_sigma_70 ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001671)

# File 'lib/biointerchange/so.rb', line 10237

def self.bacterial_RNApol_promoter_sigma_70
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001671')
end

.bacterial_RNApol_promoter_sigma_ecf ⇒ Object

A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation. (http://purl.obolibrary.org/obo/SO_0001913)

# File 'lib/biointerchange/so.rb', line 11683

def self.bacterial_RNApol_promoter_sigma_ecf
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001913')
end

.bacterial_terminator ⇒ Object

A terminator signal for bacterial transcription. (http://purl.obolibrary.org/obo/SO_0000614)

# File 'lib/biointerchange/so.rb', line 4007

def self.bacterial_terminator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000614')
end

.base ⇒ Object

A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. (http://purl.obolibrary.org/obo/SO_0001236)

# File 'lib/biointerchange/so.rb', line 7687

def self.base
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001236')
end

.base_call_error_correction ⇒ Object

A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake. (http://purl.obolibrary.org/obo/SO_0001526)

# File 'lib/biointerchange/so.rb', line 9415

def self.base_call_error_correction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001526')
end

.base_pair ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000028)

# File 'lib/biointerchange/so.rb', line 477

def self.base_pair
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000028')
end

.benign_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001770)

# File 'lib/biointerchange/so.rb', line 10831

def self.benign_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001770')
end

.beta_bulge ⇒ Object

A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees. (http://purl.obolibrary.org/obo/SO_0001107)

# File 'lib/biointerchange/so.rb', line 6913

def self.beta_bulge
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001107')
end

.beta_bulge_loop ⇒ Object

A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins. (http://purl.obolibrary.org/obo/SO_0001108)

# File 'lib/biointerchange/so.rb', line 6919

def self.beta_bulge_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001108')
end

.beta_bulge_loop_five ⇒ Object

A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3. (http://purl.obolibrary.org/obo/SO_0001109)

# File 'lib/biointerchange/so.rb', line 6925

def self.beta_bulge_loop_five
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001109')
end

.beta_bulge_loop_six ⇒ Object

A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4. (http://purl.obolibrary.org/obo/SO_0001110)

# File 'lib/biointerchange/so.rb', line 6931

def self.beta_bulge_loop_six
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001110')
end

.beta_strand ⇒ Object

A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array. (http://purl.obolibrary.org/obo/SO_0001111)

# File 'lib/biointerchange/so.rb', line 6937

def self.beta_strand
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001111')
end

.beta_turn ⇒ Object

A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization. (http://purl.obolibrary.org/obo/SO_0001133)

# File 'lib/biointerchange/so.rb', line 7069

def self.beta_turn
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001133')
end

.beta_turn_left_handed_type_one ⇒ Object

Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. (http://purl.obolibrary.org/obo/SO_0001134)

# File 'lib/biointerchange/so.rb', line 7075

def self.beta_turn_left_handed_type_one
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001134')
end

.beta_turn_left_handed_type_two ⇒ Object

Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees. (http://purl.obolibrary.org/obo/SO_0001135)

# File 'lib/biointerchange/so.rb', line 7081

def self.beta_turn_left_handed_type_two
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001135')
end

.beta_turn_right_handed_type_one ⇒ Object

Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. (http://purl.obolibrary.org/obo/SO_0001136)

# File 'lib/biointerchange/so.rb', line 7087

def self.beta_turn_right_handed_type_one
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001136')
end

.beta_turn_right_handed_type_two ⇒ Object

Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. (http://purl.obolibrary.org/obo/SO_0001137)

# File 'lib/biointerchange/so.rb', line 7093

def self.beta_turn_right_handed_type_two
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001137')
end

.beta_turn_type_eight ⇒ Object

A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees. (http://purl.obolibrary.org/obo/SO_0001155)

# File 'lib/biointerchange/so.rb', line 7201

def self.beta_turn_type_eight
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001155')
end

.beta_turn_type_six ⇒ Object

A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline. (http://purl.obolibrary.org/obo/SO_0001150)

# File 'lib/biointerchange/so.rb', line 7171

def self.beta_turn_type_six
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001150')
end

.beta_turn_type_six_a ⇒ Object

A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees. (http://purl.obolibrary.org/obo/SO_0001151)

# File 'lib/biointerchange/so.rb', line 7177

def self.beta_turn_type_six_a
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001151')
end

.beta_turn_type_six_a_one ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001152)

# File 'lib/biointerchange/so.rb', line 7183

def self.beta_turn_type_six_a_one
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001152')
end

.beta_turn_type_six_a_two ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001153)

# File 'lib/biointerchange/so.rb', line 7189

def self.beta_turn_type_six_a_two
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001153')
end

.beta_turn_type_six_b ⇒ Object

A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees. (http://purl.obolibrary.org/obo/SO_0001154)

# File 'lib/biointerchange/so.rb', line 7195

def self.beta_turn_type_six_b
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001154')
end

.bidirectional_promoter ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000568)

# File 'lib/biointerchange/so.rb', line 3731

def self.bidirectional_promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000568')
end

.binding_site ⇒ Object

A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. (http://purl.obolibrary.org/obo/SO_0000409)

# File 'lib/biointerchange/so.rb', line 2769

def self.binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000409')
end

.biochemical_region_of_peptide ⇒ Object

A region of a peptide that is involved in a biochemical function. (http://purl.obolibrary.org/obo/SO_0100001)

# File 'lib/biointerchange/so.rb', line 12353

def self.biochemical_region_of_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100001')
end

.biological_region ⇒ Object

A region defined by its disposition to be involved in a biological process. (http://purl.obolibrary.org/obo/SO_0001411)

# File 'lib/biointerchange/so.rb', line 8731

def self.biological_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001411')
end

.biomaterial_region ⇒ Object

A region which is intended for use in an experiment. (http://purl.obolibrary.org/obo/SO_0001409)

# File 'lib/biointerchange/so.rb', line 8719

def self.biomaterial_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001409')
end

.bipartite_duplication ⇒ Object

An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break. (http://purl.obolibrary.org/obo/SO_1000149)

# File 'lib/biointerchange/so.rb', line 13229

def self.bipartite_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000149')
end

.bipartite_inversion ⇒ Object

A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed). (http://purl.obolibrary.org/obo/SO_1000151)

# File 'lib/biointerchange/so.rb', line 13241

def self.bipartite_inversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000151')
end

.blocked_reading_frame ⇒ Object

A reading_frame that is interrupted by one or more stop codons; usually identified through intergenomic sequence comparisons. (http://purl.obolibrary.org/obo/SO_0000718)

# File 'lib/biointerchange/so.rb', line 4631

def self.blocked_reading_frame
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000718')
end

.blunt_end_restriction_enzyme_cleavage_junction ⇒ Object

A restriction enzyme cleavage site where both strands are cut at the same position. (http://purl.obolibrary.org/obo/SO_0001693)

# File 'lib/biointerchange/so.rb', line 10369

def self.blunt_end_restriction_enzyme_cleavage_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001693')
end

.blunt_end_restriction_enzyme_cleavage_site ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001691)

# File 'lib/biointerchange/so.rb', line 10357

def self.blunt_end_restriction_enzyme_cleavage_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001691')
end

.bound_by_factor ⇒ Object

An attribute describing a sequence that is bound by another molecule. (http://purl.obolibrary.org/obo/SO_0000277)

# File 'lib/biointerchange/so.rb', line 1983

def self.bound_by_factor
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000277')
end

.bound_by_nucleic_acid ⇒ Object

An attribute describing a sequence that is bound by a nucleic acid. (http://purl.obolibrary.org/obo/SO_0000876)

# File 'lib/biointerchange/so.rb', line 5537

def self.bound_by_nucleic_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000876')
end

.bound_by_protein ⇒ Object

An attribute describing a sequence that is bound by a protein. (http://purl.obolibrary.org/obo/SO_0000875)

# File 'lib/biointerchange/so.rb', line 5531

def self.bound_by_protein
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000875')
end

.branch_site ⇒ Object

A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat. (http://purl.obolibrary.org/obo/SO_0000611)

# File 'lib/biointerchange/so.rb', line 3989

def self.branch_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000611')
end

.BREd_motif ⇒ Object

A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G). (http://purl.obolibrary.org/obo/SO_0001663)

# File 'lib/biointerchange/so.rb', line 10189

def self.BREd_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001663')
end

.BREu_motif ⇒ Object

A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB. (http://purl.obolibrary.org/obo/SO_0000016)

# File 'lib/biointerchange/so.rb', line 411

def self.BREu_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000016')
end

.Bruno_response_element ⇒ Object

A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs. (http://purl.obolibrary.org/obo/SO_0001181)

# File 'lib/biointerchange/so.rb', line 7357

def self.Bruno_response_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001181')
end

.C_box ⇒ Object

An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn. (http://purl.obolibrary.org/obo/SO_0000622)

# File 'lib/biointerchange/so.rb', line 4055

def self.C_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000622')
end

.C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene. (http://purl.obolibrary.org/obo/SO_0000558)

# File 'lib/biointerchange/so.rb', line 3671

def self.C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000558')
end

.C_D_box_snoRNA ⇒ Object

Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'. (http://purl.obolibrary.org/obo/SO_0000593)

# File 'lib/biointerchange/so.rb', line 3881

def self.C_D_box_snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000593')
end

.C_D_box_snoRNA_encoding ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000585)

# File 'lib/biointerchange/so.rb', line 3833

def self.C_D_box_snoRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000585')
end

.C_D_box_snoRNA_primary_transcript ⇒ Object

A primary transcript encoding a small nucleolar RNA of the box C/D family. (http://purl.obolibrary.org/obo/SO_0000595)

# File 'lib/biointerchange/so.rb', line 3893

def self.C_D_box_snoRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000595')
end

.C_gene_segment ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205). (http://purl.obolibrary.org/obo/SO_0000478)

# File 'lib/biointerchange/so.rb', line 3187

def self.C_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000478')
end

.C_region ⇒ Object

The constant region of an immunoglobulin polypeptide sequence. (http://purl.obolibrary.org/obo/SO_0001834)

# File 'lib/biointerchange/so.rb', line 11209

def self.C_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001834')
end

.c_terminal_region ⇒ Object

The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa). (http://purl.obolibrary.org/obo/SO_0100015)

# File 'lib/biointerchange/so.rb', line 12437

def self.c_terminal_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100015')
end

.C_to_A_transversion ⇒ Object

A transversion from cytidine to adenine. (http://purl.obolibrary.org/obo/SO_1000019)

# File 'lib/biointerchange/so.rb', line 12557

def self.C_to_A_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000019')
end

.C_to_G_transversion ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_1000020)

# File 'lib/biointerchange/so.rb', line 12563

def self.C_to_G_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000020')
end

.C_to_T_transition ⇒ Object

A transition of a cytidine to a thymine. (http://purl.obolibrary.org/obo/SO_1000011)

# File 'lib/biointerchange/so.rb', line 12509

def self.C_to_T_transition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000011')
end

.C_to_T_transition_at_pCpG_site ⇒ Object

The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine. (http://purl.obolibrary.org/obo/SO_1000012)

# File 'lib/biointerchange/so.rb', line 12515

def self.C_to_T_transition_at_pCpG_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000012')
end

.CAAT_signal ⇒ Object

Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT. (http://purl.obolibrary.org/obo/SO_0000172)

# File 'lib/biointerchange/so.rb', line 1349

def self.CAAT_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000172')
end

.CAGE_cluster ⇒ Object

A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region. (http://purl.obolibrary.org/obo/SO_0001917)

# File 'lib/biointerchange/so.rb', line 11707

def self.CAGE_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001917')
end

.CAGE_tag ⇒ Object

A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites. (http://purl.obolibrary.org/obo/SO_0001916)

# File 'lib/biointerchange/so.rb', line 11701

def self.CAGE_tag
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001916')
end

.candidate_gene ⇒ Object

A gene suspected of being involved in the expression of a trait. (http://purl.obolibrary.org/obo/SO_0001867)

# File 'lib/biointerchange/so.rb', line 11407

def self.candidate_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001867')
end

.canonical_five_prime_splice_site ⇒ Object

The canonical 5' splice site has the sequence "GT". (SO:ke) (http://purl.obolibrary.org/obo/SO_0000677)

# File 'lib/biointerchange/so.rb', line 4385

def self.canonical_five_prime_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000677')
end

.canonical_splice_site ⇒ Object

The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively. (http://purl.obolibrary.org/obo/SO_0000675)

# File 'lib/biointerchange/so.rb', line 4373

def self.canonical_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000675')
end

.canonical_three_prime_splice_site ⇒ Object

The canonical 3' splice site has the sequence "AG". (SO:ke) (http://purl.obolibrary.org/obo/SO_0000676)

# File 'lib/biointerchange/so.rb', line 4379

def self.canonical_three_prime_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000676')
end

.cap ⇒ Object

A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA. (http://purl.obolibrary.org/obo/SO_0000581)

# File 'lib/biointerchange/so.rb', line 3809

def self.cap
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000581')
end

.capped ⇒ Object

An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end. (http://purl.obolibrary.org/obo/SO_0000146)

# File 'lib/biointerchange/so.rb', line 1193

def self.capped
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000146')
end

.capped_mRNA ⇒ Object

An mRNA that is capped. (http://purl.obolibrary.org/obo/SO_0000862)

# File 'lib/biointerchange/so.rb', line 5453

def self.capped_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000862')
end

.capped_primary_transcript ⇒ Object

A primary transcript that is capped. (http://purl.obolibrary.org/obo/SO_0000861)

# File 'lib/biointerchange/so.rb', line 5447

def self.capped_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000861')
end

.cassette_array_member ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0005847)

# File 'lib/biointerchange/so.rb', line 12281

def self.cassette_array_member
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005847')
end

.cassette_pseudogene ⇒ Object

A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy. (http://purl.obolibrary.org/obo/SO_0001434)

# File 'lib/biointerchange/so.rb', line 8863

def self.cassette_pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001434')
end

.catalytic_residue ⇒ Object

Amino acid involved in the activity of an enzyme. (http://purl.obolibrary.org/obo/SO_0001104)

# File 'lib/biointerchange/so.rb', line 6895

def self.catalytic_residue
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001104')
end

.catmat_left_handed_four ⇒ Object

A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2. (http://purl.obolibrary.org/obo/SO_0100005)

# File 'lib/biointerchange/so.rb', line 12377

def self.catmat_left_handed_four
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100005')
end

.catmat_left_handed_three ⇒ Object

A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1. (http://purl.obolibrary.org/obo/SO_0100004)

# File 'lib/biointerchange/so.rb', line 12371

def self.catmat_left_handed_three
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100004')
end

.catmat_right_handed_four ⇒ Object

A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2. (http://purl.obolibrary.org/obo/SO_0100007)

# File 'lib/biointerchange/so.rb', line 12389

def self.catmat_right_handed_four
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100007')
end

.catmat_right_handed_three ⇒ Object

A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1. (http://purl.obolibrary.org/obo/SO_0100006)

# File 'lib/biointerchange/so.rb', line 12383

def self.catmat_right_handed_three
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100006')
end

.CCA_tail ⇒ Object

Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid. (http://purl.obolibrary.org/obo/SO_0001175)

# File 'lib/biointerchange/so.rb', line 7321

def self.CCA_tail
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001175')
end

.CCAAT_motif ⇒ Object

A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels. (http://purl.obolibrary.org/obo/SO_0001856)

# File 'lib/biointerchange/so.rb', line 11341

def self.CCAAT_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001856')
end

.cDNA ⇒ Object

DNA synthesized by reverse transcriptase using RNA as a template. (http://purl.obolibrary.org/obo/SO_0000756)

# File 'lib/biointerchange/so.rb', line 4859

def self.cDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000756')
end

.cDNA_clone ⇒ Object

Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host. (http://purl.obolibrary.org/obo/SO_0000317)

# File 'lib/biointerchange/so.rb', line 2223

def self.cDNA_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000317')
end

.cDNA_match ⇒ Object

A match against cDNA sequence. (http://purl.obolibrary.org/obo/SO_0000689)

# File 'lib/biointerchange/so.rb', line 4457

def self.cDNA_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000689')
end

.CDRE_motif ⇒ Object

An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA. (http://purl.obolibrary.org/obo/SO_0001865)

# File 'lib/biointerchange/so.rb', line 11395

def self.CDRE_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001865')
end

.CDS ⇒ Object

A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. (http://purl.obolibrary.org/obo/SO_0000316)

# File 'lib/biointerchange/so.rb', line 2217

def self.CDS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000316')
end

.CDS_fragment ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001384)

# File 'lib/biointerchange/so.rb', line 8569

def self.CDS_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001384')
end

.CDS_independently_known ⇒ Object

A CDS with the evidence status of being independently known. (http://purl.obolibrary.org/obo/SO_1001246)

# File 'lib/biointerchange/so.rb', line 13463

def self.CDS_independently_known
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001246')
end

.CDS_predicted ⇒ Object

A CDS that is predicted. (http://purl.obolibrary.org/obo/SO_1001254)

# File 'lib/biointerchange/so.rb', line 13487

def self.CDS_predicted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001254')
end

.CDS_region ⇒ Object

A region of a CDS. (http://purl.obolibrary.org/obo/SO_0000851)

# File 'lib/biointerchange/so.rb', line 5387

def self.CDS_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000851')
end

.CDS_supported_by_domain_match_data ⇒ Object

A CDS that is supported by domain similarity. (http://purl.obolibrary.org/obo/SO_1001249)

# File 'lib/biointerchange/so.rb', line 13475

def self.CDS_supported_by_domain_match_data
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001249')
end

.CDS_supported_by_EST_or_cDNA_data ⇒ Object

A CDS that is supported by similarity to EST or cDNA data. (http://purl.obolibrary.org/obo/SO_1001259)

# File 'lib/biointerchange/so.rb', line 13499

def self.CDS_supported_by_EST_or_cDNA_data
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001259')
end

.CDS_supported_by_sequence_similarity_data ⇒ Object

A CDS that is supported by sequence similarity data. (http://purl.obolibrary.org/obo/SO_1001251)

# File 'lib/biointerchange/so.rb', line 13481

def self.CDS_supported_by_sequence_similarity_data
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001251')
end

.central_hydrophobic_region_of_signal_peptide ⇒ Object

The central, hydrophobic region of the signal peptide (approx 7-15 aa). (http://purl.obolibrary.org/obo/SO_0100016)

# File 'lib/biointerchange/so.rb', line 12443

def self.central_hydrophobic_region_of_signal_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100016')
end

.centromere ⇒ Object

A region of chromosome where the spindle fibers attach during mitosis and meiosis. (http://purl.obolibrary.org/obo/SO_0000577)

# File 'lib/biointerchange/so.rb', line 3785

def self.centromere
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000577')
end

.centromere_DNA_Element_I ⇒ Object

A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p). (http://purl.obolibrary.org/obo/SO_0001493)

# File 'lib/biointerchange/so.rb', line 9217

def self.centromere_DNA_Element_I
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001493')
end

.centromere_DNA_Element_II ⇒ Object

A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length. (http://purl.obolibrary.org/obo/SO_0001494)

# File 'lib/biointerchange/so.rb', line 9223

def self.centromere_DNA_Element_II
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001494')
end

.centromere_DNA_Element_III ⇒ Object

A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex. (http://purl.obolibrary.org/obo/SO_0001495)

# File 'lib/biointerchange/so.rb', line 9229

def self.centromere_DNA_Element_III
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001495')
end

.centromeric_repeat ⇒ Object

A repeat region found within the modular centromere. (http://purl.obolibrary.org/obo/SO_0001797)

# File 'lib/biointerchange/so.rb', line 10987

def self.centromeric_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001797')
end

.chimeric_cDNA_clone ⇒ Object

A cDNA clone invalidated because it is chimeric. (http://purl.obolibrary.org/obo/SO_0000810)

# File 'lib/biointerchange/so.rb', line 5153

def self.chimeric_cDNA_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000810')
end

.ChIP_seq_region ⇒ Object

A region of sequence identified by CHiP seq technology to contain a protein binding site. (http://purl.obolibrary.org/obo/SO_0001697)

# File 'lib/biointerchange/so.rb', line 10393

def self.ChIP_seq_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001697')
end

.chloroplast_chromosome ⇒ Object

A chromosome originating in a chloroplast. (http://purl.obolibrary.org/obo/SO_0000820)

# File 'lib/biointerchange/so.rb', line 5213

def self.chloroplast_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000820')
end

.chloroplast_DNA ⇒ Object

This term is used by MO. (http://purl.obolibrary.org/obo/SO_0001033)

# File 'lib/biointerchange/so.rb', line 6473

def self.chloroplast_DNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001033')
end

.chloroplast_DNA_read ⇒ Object

A sequencer read of a chloroplast DNA sample. (http://purl.obolibrary.org/obo/SO_0001930)

# File 'lib/biointerchange/so.rb', line 11785

def self.chloroplast_DNA_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001930')
end

.chloroplast_sequence ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000745)

# File 'lib/biointerchange/so.rb', line 4793

def self.chloroplast_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000745')
end

.chromoplast_chromosome ⇒ Object

A chromosome originating in a chromoplast. (http://purl.obolibrary.org/obo/SO_0000821)

# File 'lib/biointerchange/so.rb', line 5219

def self.chromoplast_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000821')
end

.chromoplast_gene ⇒ Object

A gene from chromoplast_sequence. (http://purl.obolibrary.org/obo/SO_0000093)

# File 'lib/biointerchange/so.rb', line 875

def self.chromoplast_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000093')
end

.chromoplast_sequence ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000744)

# File 'lib/biointerchange/so.rb', line 4787

def self.chromoplast_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000744')
end

.chromosomal_deletion ⇒ Object

An incomplete chromosome. (http://purl.obolibrary.org/obo/SO_1000029)

# File 'lib/biointerchange/so.rb', line 12617

def self.chromosomal_deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000029')
end

.chromosomal_duplication ⇒ Object

An extra chromosome. (http://purl.obolibrary.org/obo/SO_1000037)

# File 'lib/biointerchange/so.rb', line 12653

def self.chromosomal_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000037')
end

.chromosomal_inversion ⇒ Object

An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type. (http://purl.obolibrary.org/obo/SO_1000030)

# File 'lib/biointerchange/so.rb', line 12623

def self.chromosomal_inversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000030')
end

.chromosomal_regulatory_element ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000626)

# File 'lib/biointerchange/so.rb', line 4079

def self.chromosomal_regulatory_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000626')
end

.chromosomal_structural_element ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000628)

# File 'lib/biointerchange/so.rb', line 4091

def self.chromosomal_structural_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000628')
end

.chromosomal_translocation ⇒ Object

An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations. (http://purl.obolibrary.org/obo/SO_1000044)

# File 'lib/biointerchange/so.rb', line 12695

def self.chromosomal_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000044')
end

.chromosomal_transposition ⇒ Object

A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type. (http://purl.obolibrary.org/obo/SO_0000453)

# File 'lib/biointerchange/so.rb', line 3037

def self.chromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000453')
end

.chromosomal_variation_attribute ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001509)

# File 'lib/biointerchange/so.rb', line 9313

def self.chromosomal_variation_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001509')
end

.chromosomally_aberrant_genome ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001524)

# File 'lib/biointerchange/so.rb', line 9403

def self.chromosomally_aberrant_genome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001524')
end

.chromosome ⇒ Object

Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication. (http://purl.obolibrary.org/obo/SO_0000340)

# File 'lib/biointerchange/so.rb', line 2361

def self.chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000340')
end

.chromosome_arm ⇒ Object

A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere. (http://purl.obolibrary.org/obo/SO_0000105)

# File 'lib/biointerchange/so.rb', line 947

def self.chromosome_arm
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000105')
end

.chromosome_band ⇒ Object

A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. (http://purl.obolibrary.org/obo/SO_0000341)

# File 'lib/biointerchange/so.rb', line 2367

def self.chromosome_band
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000341')
end

.chromosome_breakage_sequence ⇒ Object

A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation. (http://purl.obolibrary.org/obo/SO_0000670)

# File 'lib/biointerchange/so.rb', line 4343

def self.chromosome_breakage_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000670')
end

.chromosome_breakpoint ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001021)

# File 'lib/biointerchange/so.rb', line 6401

def self.chromosome_breakpoint
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001021')
end

.chromosome_fission ⇒ Object

A chromosome that occurred by the division of a larger chromosome. (http://purl.obolibrary.org/obo/SO_1000141)

# File 'lib/biointerchange/so.rb', line 13181

def self.chromosome_fission
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000141')
end

.chromosome_number_variation ⇒ Object

A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. (http://purl.obolibrary.org/obo/SO_1000182)

# File 'lib/biointerchange/so.rb', line 13349

def self.chromosome_number_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000182')
end

.chromosome_part ⇒ Object

A region of a chromosome. (http://purl.obolibrary.org/obo/SO_0000830)

# File 'lib/biointerchange/so.rb', line 5261

def self.chromosome_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000830')
end

.chromosome_structure_variation ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_1000183)

# File 'lib/biointerchange/so.rb', line 13355

def self.chromosome_structure_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000183')
end

.chromosome_variation ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000240)

# File 'lib/biointerchange/so.rb', line 1761

def self.chromosome_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000240')
end

.circular ⇒ Object

A quality of a nucleotide polymer that has no terminal nucleotide residues. (http://purl.obolibrary.org/obo/SO_0000988)

# File 'lib/biointerchange/so.rb', line 6203

def self.circular
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000988')
end

.circular_double_stranded_DNA_chromosome ⇒ Object

Structural unit composed of a self-replicating, double-stranded, circular DNA molecule. (http://purl.obolibrary.org/obo/SO_0000958)

# File 'lib/biointerchange/so.rb', line 6029

def self.circular_double_stranded_DNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000958')
end

.circular_double_stranded_RNA_chromosome ⇒ Object

Structural unit composed of a self-replicating, double-stranded, circular RNA molecule. (http://purl.obolibrary.org/obo/SO_0000967)

# File 'lib/biointerchange/so.rb', line 6083

def self.circular_double_stranded_RNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000967')
end

.circular_single_stranded_DNA_chromosome ⇒ Object

Structural unit composed of a self-replicating, single-stranded, circular DNA molecule. (http://purl.obolibrary.org/obo/SO_0000960)

# File 'lib/biointerchange/so.rb', line 6041

def self.circular_single_stranded_DNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000960')
end

.circular_single_stranded_RNA_chromosome ⇒ Object

Structural unit composed of a self-replicating, single-stranded, circular DNA molecule. (http://purl.obolibrary.org/obo/SO_0000966)

# File 'lib/biointerchange/so.rb', line 6077

def self.circular_single_stranded_RNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000966')
end

.cis_regulatory_frameshift_element ⇒ Object

A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence. (http://purl.obolibrary.org/obo/SO_0001427)

# File 'lib/biointerchange/so.rb', line 8827

def self.cis_regulatory_frameshift_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001427')
end

.cis_splice_site ⇒ Object

Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron. (http://purl.obolibrary.org/obo/SO_0001419)

# File 'lib/biointerchange/so.rb', line 8779

def self.cis_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001419')
end

.class_I_RNA ⇒ Object

Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm. (http://purl.obolibrary.org/obo/SO_0000990)

# File 'lib/biointerchange/so.rb', line 6215

def self.class_I_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000990')
end

.class_II_RNA ⇒ Object

Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm. (http://purl.obolibrary.org/obo/SO_0000989)

# File 'lib/biointerchange/so.rb', line 6209

def self.class_II_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000989')
end

.cleaved_for_gpi_anchor_region ⇒ Object

The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor. (http://purl.obolibrary.org/obo/SO_0001408)

# File 'lib/biointerchange/so.rb', line 8713

def self.cleaved_for_gpi_anchor_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001408')
end

.cleaved_initiator_methionine ⇒ Object

The initiator methionine that has been cleaved from a mature polypeptide sequence. (http://purl.obolibrary.org/obo/SO_0000691)

# File 'lib/biointerchange/so.rb', line 4469

def self.cleaved_initiator_methionine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000691')
end

.cleaved_peptide_region ⇒ Object

The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation. (http://purl.obolibrary.org/obo/SO_0100011)

# File 'lib/biointerchange/so.rb', line 12413

def self.cleaved_peptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100011')
end

.clip ⇒ Object

Part of the primary transcript that is clipped off during processing. (http://purl.obolibrary.org/obo/SO_0000303)

# File 'lib/biointerchange/so.rb', line 2139

def self.clip
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000303')
end

.clone ⇒ Object

A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism. (http://purl.obolibrary.org/obo/SO_0000151)

# File 'lib/biointerchange/so.rb', line 1223

def self.clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000151')
end

.clone_attribute ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000787)

# File 'lib/biointerchange/so.rb', line 5039

def self.clone_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000787')
end

.clone_end ⇒ Object

A read from an end of the clone sequence. (http://purl.obolibrary.org/obo/SO_0001793)

# File 'lib/biointerchange/so.rb', line 10963

def self.clone_end
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001793')
end

.clone_insert ⇒ Object

The region of sequence that has been inserted and is being propagated by the clone. (http://purl.obolibrary.org/obo/SO_0000753)

# File 'lib/biointerchange/so.rb', line 4841

def self.clone_insert
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000753')
end

.clone_insert_end ⇒ Object

The end of the clone insert. (http://purl.obolibrary.org/obo/SO_0000103)

# File 'lib/biointerchange/so.rb', line 935

def self.clone_insert_end
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000103')
end

.clone_insert_start ⇒ Object

Either:

The start of the clone insert.
(http://purl.obolibrary.org/obo/SO_0000179)

Or:

-- No comment or description provided. --
(http://purl.obolibrary.org/obo/SO_0000767)

# File 'lib/biointerchange/so.rb', line 1395

def self.clone_insert_start
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000179'), RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000767') ]
end

.cloned ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000788)

# File 'lib/biointerchange/so.rb', line 5045

def self.cloned
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000788')
end

.cloned_cDNA ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000792)

# File 'lib/biointerchange/so.rb', line 5069

def self.cloned_cDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000792')
end

.cloned_cDNA_insert ⇒ Object

A clone insert made from cDNA. (http://purl.obolibrary.org/obo/SO_0000913)

# File 'lib/biointerchange/so.rb', line 5759

def self.cloned_cDNA_insert
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000913')
end

.cloned_genomic ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000791)

# File 'lib/biointerchange/so.rb', line 5063

def self.cloned_genomic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000791')
end

.cloned_genomic_insert ⇒ Object

A clone insert made from genomic DNA. (http://purl.obolibrary.org/obo/SO_0000914)

# File 'lib/biointerchange/so.rb', line 5765

def self.cloned_genomic_insert
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000914')
end

.cloned_region ⇒ Object

Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions. (http://purl.obolibrary.org/obo/SO_0000785)

# File 'lib/biointerchange/so.rb', line 5027

def self.cloned_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000785')
end

.coding_conserved_region ⇒ Object

Coding region of sequence similarity by descent from a common ancestor. (http://purl.obolibrary.org/obo/SO_0000332)

# File 'lib/biointerchange/so.rb', line 2313

def self.coding_conserved_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000332')
end

.coding_end ⇒ Object

The last base to be translated into protein. It does not include the stop codon. (http://purl.obolibrary.org/obo/SO_0000327)

# File 'lib/biointerchange/so.rb', line 2283

def self.coding_end
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000327')
end

.coding_exon ⇒ Object

An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon). (http://purl.obolibrary.org/obo/SO_0000195)

# File 'lib/biointerchange/so.rb', line 1491

def self.coding_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000195')
end

.coding_region_of_exon ⇒ Object

The region of an exon that encodes for protein sequence. (http://purl.obolibrary.org/obo/SO_0001215)

# File 'lib/biointerchange/so.rb', line 7561

def self.coding_region_of_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001215')
end

.coding_sequence_variant ⇒ Object

A sequence variant that changes the coding sequence. (http://purl.obolibrary.org/obo/SO_0001580)

# File 'lib/biointerchange/so.rb', line 9739

def self.coding_sequence_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001580')
end

.coding_start ⇒ Object

The first base to be translated into protein. (http://purl.obolibrary.org/obo/SO_0000323)

# File 'lib/biointerchange/so.rb', line 2259

def self.coding_start
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000323')
end

.coding_transcript_intron_variant ⇒ Object

A transcript variant occurring within an intron of a coding transcript. (http://purl.obolibrary.org/obo/SO_0001969)

# File 'lib/biointerchange/so.rb', line 12023

def self.coding_transcript_intron_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001969')
end

.coding_transcript_variant ⇒ Object

A transcript variant of a protein coding gene. (http://purl.obolibrary.org/obo/SO_0001968)

# File 'lib/biointerchange/so.rb', line 12017

def self.coding_transcript_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001968')
end

.coding_variant_quality ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001814)

# File 'lib/biointerchange/so.rb', line 11089

def self.coding_variant_quality
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001814')
end

.codon ⇒ Object

A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS. (http://purl.obolibrary.org/obo/SO_0000360)

# File 'lib/biointerchange/so.rb', line 2475

def self.codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000360')
end

.codon_redefined ⇒ Object

An attribute describing the alteration of codon meaning. (http://purl.obolibrary.org/obo/SO_0000882)

# File 'lib/biointerchange/so.rb', line 5573

def self.codon_redefined
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000882')
end

.coiled_coil ⇒ Object

A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope. (http://purl.obolibrary.org/obo/SO_0001080)

# File 'lib/biointerchange/so.rb', line 6751

def self.coiled_coil
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001080')
end

.cointegrated_plasmid ⇒ Object

A MGE region consisting of two fused plasmids resulting from a replicative transposition event. (http://purl.obolibrary.org/obo/SO_0001045)

# File 'lib/biointerchange/so.rb', line 6545

def self.cointegrated_plasmid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001045')
end

.common_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001767)

# File 'lib/biointerchange/so.rb', line 10813

def self.common_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001767')
end

.compensatory_transcript_secondary_structure_variant ⇒ Object

A secondary structure variant that compensate for the change made by a previous variant. (http://purl.obolibrary.org/obo/SO_0001597)

# File 'lib/biointerchange/so.rb', line 9823

def self.compensatory_transcript_secondary_structure_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001597')
end

.complete_evidence_for_feature ⇒ Object

B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A. (http://purl.obolibrary.org/obo/so_2_5_2.obo#complete_evidence_for_feature)

# File 'lib/biointerchange/so.rb', line 29

def self.complete_evidence_for_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#complete_evidence_for_feature')
end

.complex_3D_structural_variant ⇒ Object

A sequence variant that changes the resulting polypeptide structure. (http://purl.obolibrary.org/obo/SO_0001600)

# File 'lib/biointerchange/so.rb', line 9841

def self.complex_3D_structural_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001600')
end

.complex_change_of_translational_product_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001602)

# File 'lib/biointerchange/so.rb', line 9853

def self.complex_change_of_translational_product_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001602')
end

.complex_chromosomal_mutation ⇒ Object

A chromosome structure variant with 4 or more breakpoints. (http://purl.obolibrary.org/obo/SO_1000146)

# File 'lib/biointerchange/so.rb', line 13211

def self.complex_chromosomal_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000146')
end

.complex_structural_alteration ⇒ Object

A structural sequence alteration or rearrangement encompassing one or more genome fragments. (http://purl.obolibrary.org/obo/SO_0001784)

# File 'lib/biointerchange/so.rb', line 10909

def self.complex_structural_alteration
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001784')
end

.complex_substitution ⇒ Object

When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change. (EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html) (http://purl.obolibrary.org/obo/SO_1000005)

# File 'lib/biointerchange/so.rb', line 12485

def self.complex_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000005')
end

.complex_transcript_variant ⇒ Object

A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border. (http://purl.obolibrary.org/obo/SO_0001577)

# File 'lib/biointerchange/so.rb', line 9721

def self.complex_transcript_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001577')
end

.compositionally_biased_region_of_peptide ⇒ Object

Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length. (http://purl.obolibrary.org/obo/SO_0001066)

# File 'lib/biointerchange/so.rb', line 6673

def self.compositionally_biased_region_of_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001066')
end

.compound_chromosome ⇒ Object

A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms. (http://purl.obolibrary.org/obo/SO_1000042)

# File 'lib/biointerchange/so.rb', line 12683

def self.compound_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000042')
end

.compound_chromosome_arm ⇒ Object

FLAG - this term is should probably be a part of rather than an is_a. (http://purl.obolibrary.org/obo/SO_0000060)

# File 'lib/biointerchange/so.rb', line 677

def self.compound_chromosome_arm
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000060')
end

.computed_feature ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000309)

# File 'lib/biointerchange/so.rb', line 2175

def self.computed_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000309')
end

.computed_feature_by_similarity ⇒ Object

. (http://purl.obolibrary.org/obo/SO_0000311)

# File 'lib/biointerchange/so.rb', line 2187

def self.computed_feature_by_similarity
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000311')
end

.conformational_change_variant ⇒ Object

A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence. (http://purl.obolibrary.org/obo/SO_0001601)

# File 'lib/biointerchange/so.rb', line 9847

def self.conformational_change_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001601')
end

.conformational_switch ⇒ Object

A region of a polypeptide, involved in the transition from one conformational state to another. (http://purl.obolibrary.org/obo/SO_0001422)

# File 'lib/biointerchange/so.rb', line 8797

def self.conformational_switch
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001422')
end

.conjugative_transposon ⇒ Object

A transposon that encodes function required for conjugation. (http://purl.obolibrary.org/obo/SO_0000371)

# File 'lib/biointerchange/so.rb', line 2541

def self.conjugative_transposon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000371')
end

.connects_on ⇒ Object

X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z. (http://purl.obolibrary.org/obo/so_2_5_2.obo#connects_on)

# File 'lib/biointerchange/so.rb', line 35

def self.connects_on
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#connects_on')
end

.consensus ⇒ Object

Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA. (http://purl.obolibrary.org/obo/SO_0000993)

# File 'lib/biointerchange/so.rb', line 6233

def self.consensus
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000993')
end

.consensus_AFLP_fragment ⇒ Object

A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input. (http://purl.obolibrary.org/obo/SO_0001991)

# File 'lib/biointerchange/so.rb', line 12149

def self.consensus_AFLP_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001991')
end

.consensus_gDNA ⇒ Object

Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input. (http://purl.obolibrary.org/obo/SO_0001931)

# File 'lib/biointerchange/so.rb', line 11791

def self.consensus_gDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001931')
end

.consensus_mRNA ⇒ Object

DO not obsolete without considering MGED mapping. (http://purl.obolibrary.org/obo/SO_0000995)

# File 'lib/biointerchange/so.rb', line 6245

def self.consensus_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000995')
end

.consensus_region ⇒ Object

DO not obsolete without considering MGED mapping. (http://purl.obolibrary.org/obo/SO_0000994)

# File 'lib/biointerchange/so.rb', line 6239

def self.consensus_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000994')
end

.conservative_amino_acid_substitution ⇒ Object

A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide. (http://purl.obolibrary.org/obo/SO_0001607)

# File 'lib/biointerchange/so.rb', line 9883

def self.conservative_amino_acid_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001607')
end

.conservative_inframe_deletion ⇒ Object

An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons. (http://purl.obolibrary.org/obo/SO_0001825)

# File 'lib/biointerchange/so.rb', line 11155

def self.conservative_inframe_deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001825')
end

.conservative_inframe_insertion ⇒ Object

An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons. (http://purl.obolibrary.org/obo/SO_0001823)

# File 'lib/biointerchange/so.rb', line 11143

def self.conservative_inframe_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001823')
end

.conservative_missense_variant ⇒ Object

A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious. (http://purl.obolibrary.org/obo/SO_0001585)

# File 'lib/biointerchange/so.rb', line 9757

def self.conservative_missense_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001585')
end

.conserved ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000856)

# File 'lib/biointerchange/so.rb', line 5417

def self.conserved
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000856')
end

.conserved_region ⇒ Object

Region of sequence similarity by descent from a common ancestor. (http://purl.obolibrary.org/obo/SO_0000330)

# File 'lib/biointerchange/so.rb', line 2301

def self.conserved_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000330')
end

.contained_by ⇒ Object

X contained_by Y iff X starts after start of Y and X ends before end of Y. (http://purl.obolibrary.org/obo/so_2_5_2.obo#contained_by)

# File 'lib/biointerchange/so.rb', line 41

def self.contained_by
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#contained_by')
end

.contains ⇒ Object

The inverse of contained_by. (http://purl.obolibrary.org/obo/so_2_5_2.obo#contains)

# File 'lib/biointerchange/so.rb', line 47

def self.contains
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#contains')
end

.contig ⇒ Object

A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. (http://purl.obolibrary.org/obo/SO_0000149)

# File 'lib/biointerchange/so.rb', line 1211

def self.contig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000149')
end

.contig_collection ⇒ Object

A collection of contigs. (http://purl.obolibrary.org/obo/SO_0001462)

# File 'lib/biointerchange/so.rb', line 9031

def self.contig_collection
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001462')
end

.contig_read ⇒ Object

A DNA sequencer read which is part of a contig. (http://purl.obolibrary.org/obo/SO_0000476)

# File 'lib/biointerchange/so.rb', line 3175

def self.contig_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000476')
end

.copy_number_change ⇒ Object

A sequence variant where copies of a feature (CNV) are either increased or decreased. (http://purl.obolibrary.org/obo/SO_0001563)

# File 'lib/biointerchange/so.rb', line 9637

def self.copy_number_change
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001563')
end

.copy_number_decrease ⇒ Object

A sequence variant where copies of a feature are decreased relative to the reference. (http://purl.obolibrary.org/obo/SO_0001912)

# File 'lib/biointerchange/so.rb', line 11677

def self.copy_number_decrease
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001912')
end

.copy_number_gain ⇒ Object

A sequence alteration whereby the copy number of a given regions is greater than the reference sequence. (http://purl.obolibrary.org/obo/SO_0001742)

# File 'lib/biointerchange/so.rb', line 10663

def self.copy_number_gain
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001742')
end

.copy_number_increase ⇒ Object

A sequence variant where copies of a feature are increased relative to the reference. (http://purl.obolibrary.org/obo/SO_0001911)

# File 'lib/biointerchange/so.rb', line 11671

def self.copy_number_increase
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001911')
end

.copy_number_loss ⇒ Object

A sequence alteration whereby the copy number of a given region is less than the reference sequence. (http://purl.obolibrary.org/obo/SO_0001743)

# File 'lib/biointerchange/so.rb', line 10669

def self.copy_number_loss
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001743')
end

.copy_number_variation ⇒ Object

A variation that increases or decreases the copy number of a given region. (http://purl.obolibrary.org/obo/SO_0001019)

# File 'lib/biointerchange/so.rb', line 6389

def self.copy_number_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001019')
end

.core_promoter_element ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001660)

# File 'lib/biointerchange/so.rb', line 10171

def self.core_promoter_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001660')
end

.cosmid ⇒ Object

A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites. (http://purl.obolibrary.org/obo/SO_0000156)

# File 'lib/biointerchange/so.rb', line 1253

def self.cosmid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000156')
end

.cosmid_clone ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000765)

# File 'lib/biointerchange/so.rb', line 4913

def self.cosmid_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000765')
end

.covalent_binding_site ⇒ Object

Binding involving a covalent bond. (http://purl.obolibrary.org/obo/SO_0001090)

# File 'lib/biointerchange/so.rb', line 6811

def self.covalent_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001090')
end

.CpG_island ⇒ Object

Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes. (http://purl.obolibrary.org/obo/SO_0000307)

# File 'lib/biointerchange/so.rb', line 2163

def self.CpG_island
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000307')
end

.CRE ⇒ Object

A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors. (http://purl.obolibrary.org/obo/SO_0001843)

# File 'lib/biointerchange/so.rb', line 11263

def self.CRE
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001843')
end

.CRISPR ⇒ Object

Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences. (http://purl.obolibrary.org/obo/SO_0001459)

# File 'lib/biointerchange/so.rb', line 9013

def self.CRISPR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001459')
end

.CRM ⇒ Object

A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. (http://purl.obolibrary.org/obo/SO_0000727)

# File 'lib/biointerchange/so.rb', line 4685

def self.CRM
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000727')
end

.cross_genome_match ⇒ Object

A nucleotide match against a sequence from another organism. (http://purl.obolibrary.org/obo/SO_0000177)

# File 'lib/biointerchange/so.rb', line 1379

def self.cross_genome_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000177')
end

.cross_link ⇒ Object

Posttranslationally formed amino acid bonds. (http://purl.obolibrary.org/obo/SO_0001087)

# File 'lib/biointerchange/so.rb', line 6793

def self.cross_link
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001087')
end

.cryptic ⇒ Object

A feature_attribute describing a feature that is not manifest under normal conditions. (http://purl.obolibrary.org/obo/SO_0000976)

# File 'lib/biointerchange/so.rb', line 6131

def self.cryptic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000976')
end

.cryptic_gene ⇒ Object

A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning. (http://purl.obolibrary.org/obo/SO_0001431)

# File 'lib/biointerchange/so.rb', line 8845

def self.cryptic_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001431')
end

.cryptic_prophage ⇒ Object

A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes. (GOC:jl) (http://purl.obolibrary.org/obo/SO_0001007)

# File 'lib/biointerchange/so.rb', line 6317

def self.cryptic_prophage
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001007')
end

.cryptic_splice_acceptor ⇒ Object

A sequence variant whereby a new splice site is created due to the activation of a new acceptor. (http://purl.obolibrary.org/obo/SO_0001570)

# File 'lib/biointerchange/so.rb', line 9679

def self.cryptic_splice_acceptor
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001570')
end

.cryptic_splice_donor ⇒ Object

A sequence variant whereby a new splice site is created due to the activation of a new donor. (http://purl.obolibrary.org/obo/SO_0001571)

# File 'lib/biointerchange/so.rb', line 9685

def self.cryptic_splice_donor
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001571')
end

.cryptic_splice_site ⇒ Object

A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error. (http://purl.obolibrary.org/obo/SO_0001533)

# File 'lib/biointerchange/so.rb', line 9457

def self.cryptic_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001533')
end

.cryptic_splice_site_variant ⇒ Object

A sequence variant causing a new (functional) splice site. (http://purl.obolibrary.org/obo/SO_0001569)

# File 'lib/biointerchange/so.rb', line 9673

def self.cryptic_splice_site_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001569')
end

.cryptogene ⇒ Object

A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence. (http://purl.obolibrary.org/obo/SO_1001196)

# File 'lib/biointerchange/so.rb', line 13439

def self.cryptogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001196')
end

.CSL_response_element ⇒ Object

A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors. (http://purl.obolibrary.org/obo/SO_0001839)

# File 'lib/biointerchange/so.rb', line 11239

def self.CSL_response_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001839')
end

.CsrB_RsmB_RNA ⇒ Object

An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family. (http://purl.obolibrary.org/obo/SO_0000377)

# File 'lib/biointerchange/so.rb', line 2577

def self.CsrB_RsmB_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000377')
end

.ct_gene ⇒ Object

A gene from chloroplast sequence. (http://purl.obolibrary.org/obo/SO_0000092)

# File 'lib/biointerchange/so.rb', line 869

def self.ct_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000092')
end

.CTCF_binding_site ⇒ Object

A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor. (http://purl.obolibrary.org/obo/SO_0001974)

# File 'lib/biointerchange/so.rb', line 12053

def self.CTCF_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001974')
end

.CTG_start_codon ⇒ Object

A non-canonical start codon of sequence CTG. (http://purl.obolibrary.org/obo/SO_1001273)

# File 'lib/biointerchange/so.rb', line 13583

def self.CTG_start_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001273')
end

.CuRE ⇒ Object

A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast). (http://purl.obolibrary.org/obo/SO_0001844)

# File 'lib/biointerchange/so.rb', line 11269

def self.CuRE
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001844')
end

.cyanelle_chromosome ⇒ Object

A chromosome originating in a cyanelle. (http://purl.obolibrary.org/obo/SO_0000822)

# File 'lib/biointerchange/so.rb', line 5225

def self.cyanelle_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000822')
end

.cyanelle_gene ⇒ Object

A gene from cyanelle sequence. (http://purl.obolibrary.org/obo/SO_0000094)

# File 'lib/biointerchange/so.rb', line 881

def self.cyanelle_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000094')
end

.cyanelle_sequence ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000746)

# File 'lib/biointerchange/so.rb', line 4799

def self.cyanelle_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000746')
end

.cyclic_translocation ⇒ Object

A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third. (http://purl.obolibrary.org/obo/SO_1000150)

# File 'lib/biointerchange/so.rb', line 13235

def self.cyclic_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000150')
end

.cysteine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001447)

# File 'lib/biointerchange/so.rb', line 8941

def self.cysteine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001447')
end

.cysteine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding cysteinyl tRNA (SO:0000258). (http://purl.obolibrary.org/obo/SO_0000215)

# File 'lib/biointerchange/so.rb', line 1611

def self.cysteine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000215')
end

.cysteinyl_tRNA ⇒ Object

A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region. (http://purl.obolibrary.org/obo/SO_0000258)

# File 'lib/biointerchange/so.rb', line 1869

def self.cysteinyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000258')
end

.cytoplasmic_polypeptide_region ⇒ Object

Polypeptide region that is localized inside the cytoplasm. (http://purl.obolibrary.org/obo/SO_0001073)

# File 'lib/biointerchange/so.rb', line 6709

def self.cytoplasmic_polypeptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001073')
end

.D_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene. (http://purl.obolibrary.org/obo/SO_0000559)

# File 'lib/biointerchange/so.rb', line 3677

def self.D_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000559')
end

.D_DJ_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000504)

# File 'lib/biointerchange/so.rb', line 3343

def self.D_DJ_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000504')
end

.D_DJ_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene. (http://purl.obolibrary.org/obo/SO_0000505)

# File 'lib/biointerchange/so.rb', line 3349

def self.D_DJ_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000505')
end

.D_DJ_J_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000506)

# File 'lib/biointerchange/so.rb', line 3355

def self.D_DJ_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000506')
end

.D_DJ_J_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene. (http://purl.obolibrary.org/obo/SO_0000508)

# File 'lib/biointerchange/so.rb', line 3367

def self.D_DJ_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000508')
end

.D_gene_recombination_feature ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000492)

# File 'lib/biointerchange/so.rb', line 3271

def self.D_gene_recombination_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000492')
end

.D_gene_segment ⇒ Object

Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment. (http://purl.obolibrary.org/obo/SO_0000458)

# File 'lib/biointerchange/so.rb', line 3067

def self.D_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000458')
end

.D_J_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000509)

# File 'lib/biointerchange/so.rb', line 3373

def self.D_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000509')
end

.D_J_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene. (http://purl.obolibrary.org/obo/SO_0000560)

# File 'lib/biointerchange/so.rb', line 3683

def self.D_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000560')
end

.D_loop ⇒ Object

Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein. (http://purl.obolibrary.org/obo/SO_0000297)

# File 'lib/biointerchange/so.rb', line 2103

def self.D_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000297')
end

.DArT_marker ⇒ Object

A genetic marker, discovered using Diversity Arrays Technology (DArT) technology. (http://purl.obolibrary.org/obo/SO_0001646)

# File 'lib/biointerchange/so.rb', line 10111

def self.DArT_marker
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001646')
end

.databank_entry ⇒ Object

The sequence referred to by an entry in a databank such as Genbank or SwissProt. (http://purl.obolibrary.org/obo/SO_2000061)

# File 'lib/biointerchange/so.rb', line 13667

def self.databank_entry
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_2000061')
end

.dCAPS_primer ⇒ Object

A primer with one or more mis-matches to the DNA template corresponding to a position within a restriction enzyme recognition site. (http://purl.obolibrary.org/obo/SO_0001699)

# File 'lib/biointerchange/so.rb', line 10405

def self.dCAPS_primer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001699')
end

.DCE ⇒ Object

A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII. (http://purl.obolibrary.org/obo/SO_0001664)

# File 'lib/biointerchange/so.rb', line 10195

def self.DCE
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001664')
end

.DCE_SI ⇒ Object

A sub element of the DCE core promoter element, with consensus sequence CTTC. (http://purl.obolibrary.org/obo/SO_0001665)

# File 'lib/biointerchange/so.rb', line 10201

def self.DCE_SI
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001665')
end

.DCE_SII ⇒ Object

A sub element of the DCE core promoter element with consensus sequence CTGT. (http://purl.obolibrary.org/obo/SO_0001666)

# File 'lib/biointerchange/so.rb', line 10207

def self.DCE_SII
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001666')
end

.DCE_SIII ⇒ Object

A sub element of the DCE core promoter element with consensus sequence AGC. (http://purl.obolibrary.org/obo/SO_0001667)

# File 'lib/biointerchange/so.rb', line 10213

def self.DCE_SIII
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001667')
end

.DDB_box ⇒ Object

A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases. (http://purl.obolibrary.org/obo/SO_0001804)

# File 'lib/biointerchange/so.rb', line 11029

def self.DDB_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001804')
end

.de_novo_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001781)

# File 'lib/biointerchange/so.rb', line 10897

def self.de_novo_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001781')
end

.decayed_exon ⇒ Object

A non-functional descendant of an exon. (http://purl.obolibrary.org/obo/SO_0000464)

# File 'lib/biointerchange/so.rb', line 3103

def self.decayed_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000464')
end

.decreased_polyadenylation_variant ⇒ Object

A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference. (http://purl.obolibrary.org/obo/SO_0001803)

# File 'lib/biointerchange/so.rb', line 11023

def self.decreased_polyadenylation_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001803')
end

.decreased_transcript_level_variant ⇒ Object

A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001541)

# File 'lib/biointerchange/so.rb', line 9505

def self.decreased_transcript_level_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001541')
end

.decreased_transcript_stability_variant ⇒ Object

A sequence variant that decreases transcript stability with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001547)

# File 'lib/biointerchange/so.rb', line 9541

def self.decreased_transcript_stability_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001547')
end

.decreased_transcription_rate_variant ⇒ Object

A sequence variant that decreases the rate of transcription with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001552)

# File 'lib/biointerchange/so.rb', line 9571

def self.decreased_transcription_rate_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001552')
end

.decreased_translational_product_level ⇒ Object

A sequence variant which decreases the translational product level with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001555)

# File 'lib/biointerchange/so.rb', line 9589

def self.decreased_translational_product_level
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001555')
end

.defective_conjugative_transposon ⇒ Object

An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon. (http://purl.obolibrary.org/obo/SO_0001049)

# File 'lib/biointerchange/so.rb', line 6569

def self.defective_conjugative_transposon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001049')
end

.deficient_interchromosomal_transposition ⇒ Object

An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining. (http://purl.obolibrary.org/obo/SO_0000063)

# File 'lib/biointerchange/so.rb', line 695

def self.deficient_interchromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000063')
end

.deficient_intrachromosomal_transposition ⇒ Object

An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining. (http://purl.obolibrary.org/obo/SO_0000062)

# File 'lib/biointerchange/so.rb', line 689

def self.deficient_intrachromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000062')
end

.deficient_inversion ⇒ Object

A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted. (http://purl.obolibrary.org/obo/SO_1000171)

# File 'lib/biointerchange/so.rb', line 13319

def self.deficient_inversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000171')
end

.deficient_translocation ⇒ Object

A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining. (http://purl.obolibrary.org/obo/SO_1000147)

# File 'lib/biointerchange/so.rb', line 13217

def self.deficient_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000147')
end

.delete ⇒ Object

To remove a subsection of sequence. (http://purl.obolibrary.org/obo/SO_0000045)

# File 'lib/biointerchange/so.rb', line 579

def self.delete
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000045')
end

.delete_U ⇒ Object

An edit to delete a uridine. (http://purl.obolibrary.org/obo/SO_0000918)

# File 'lib/biointerchange/so.rb', line 5789

def self.delete_U
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000918')
end

.deletion ⇒ Object

The point at which one or more contiguous nucleotides were excised. (http://purl.obolibrary.org/obo/SO_0000159)

# File 'lib/biointerchange/so.rb', line 1271

def self.deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000159')
end

.deletion_breakpoint ⇒ Object

The point within a chromosome where a deletion begins or ends. (http://purl.obolibrary.org/obo/SO_0001415)

# File 'lib/biointerchange/so.rb', line 8755

def self.deletion_breakpoint
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001415')
end

.deletion_junction ⇒ Object

The space between two bases in a sequence which marks the position where a deletion has occurred. (http://purl.obolibrary.org/obo/SO_0000687)

# File 'lib/biointerchange/so.rb', line 4445

def self.deletion_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000687')
end

.derives_from ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#derives_from)

# File 'lib/biointerchange/so.rb', line 53

def self.derives_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#derives_from')
end

.designed_sequence ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000546)

# File 'lib/biointerchange/so.rb', line 3595

def self.designed_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000546')
end

.destruction_box ⇒ Object

A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN. (http://purl.obolibrary.org/obo/SO_0001805)

# File 'lib/biointerchange/so.rb', line 11035

def self.destruction_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001805')
end

.dexstrosynaptic_chromosome ⇒ Object

An autosynaptic chromosome carrying the two right (D = dextro) telomeres. (http://purl.obolibrary.org/obo/SO_1000142)

# File 'lib/biointerchange/so.rb', line 13187

def self.dexstrosynaptic_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000142')
end

.dg_repeat ⇒ Object

A repeat region which is part of the regional centromere outer repeat region. (http://purl.obolibrary.org/obo/SO_0001898)

# File 'lib/biointerchange/so.rb', line 11593

def self.dg_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001898')
end

.dh_repeat ⇒ Object

A repeat region which is part of the regional centromere outer repeat region. (http://purl.obolibrary.org/obo/SO_0001899)

# File 'lib/biointerchange/so.rb', line 11599

def self.dh_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001899')
end

.DHU_loop ⇒ Object

Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues. (http://purl.obolibrary.org/obo/SO_0001176)

# File 'lib/biointerchange/so.rb', line 7327

def self.DHU_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001176')
end

.dicistronic ⇒ Object

An attribute describing a sequence that contains the code for two gene products. (http://purl.obolibrary.org/obo/SO_0000879)

# File 'lib/biointerchange/so.rb', line 5555

def self.dicistronic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000879')
end

.dicistronic_mRNA ⇒ Object

An mRNA that has the quality dicistronic. (http://purl.obolibrary.org/obo/SO_0000716)

# File 'lib/biointerchange/so.rb', line 4619

def self.dicistronic_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000716')
end

.dicistronic_primary_transcript ⇒ Object

A primary transcript that has the quality dicistronic. (http://purl.obolibrary.org/obo/SO_1001197)

# File 'lib/biointerchange/so.rb', line 13445

def self.dicistronic_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001197')
end

.dicistronic_transcript ⇒ Object

A transcript that is dicistronic. (http://purl.obolibrary.org/obo/SO_0000079)

# File 'lib/biointerchange/so.rb', line 791

def self.dicistronic_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000079')
end

.dif_site ⇒ Object

A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase. (http://purl.obolibrary.org/obo/SO_0000949)

# File 'lib/biointerchange/so.rb', line 5975

def self.dif_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000949')
end

.dihydrouridine ⇒ Object

A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring. (http://purl.obolibrary.org/obo/SO_0001228)

# File 'lib/biointerchange/so.rb', line 7639

def self.dihydrouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001228')
end

.dinucleotide_repeat_microsatellite_feature ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000290)

# File 'lib/biointerchange/so.rb', line 2061

def self.dinucleotide_repeat_microsatellite_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000290')
end

.diplotype ⇒ Object

A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known. (http://purl.obolibrary.org/obo/SO_0001028)

# File 'lib/biointerchange/so.rb', line 6443

def self.diplotype
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001028')
end

.direct ⇒ Object

A quality of an insertion where the insert is not in a cytologically inverted orientation. (http://purl.obolibrary.org/obo/SO_0001514)

# File 'lib/biointerchange/so.rb', line 9343

def self.direct
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001514')
end

.direct_repeat ⇒ Object

A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA. (http://purl.obolibrary.org/obo/SO_0000314)

# File 'lib/biointerchange/so.rb', line 2205

def self.direct_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000314')
end

.direct_tandem_duplication ⇒ Object

A tandem duplication where the individual regions are in the same orientation. (http://purl.obolibrary.org/obo/SO_1000039)

# File 'lib/biointerchange/so.rb', line 12665

def self.direct_tandem_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000039')
end

.direction_attribute ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001029)

# File 'lib/biointerchange/so.rb', line 6449

def self.direction_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001029')
end

.disconnected_from ⇒ Object

X is disconnected_from Y iff it is not the case that X overlaps Y. (http://purl.obolibrary.org/obo/so_2_5_2.obo#disconnected_from)

# File 'lib/biointerchange/so.rb', line 59

def self.disconnected_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#disconnected_from')
end

.disease_associated_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001771)

# File 'lib/biointerchange/so.rb', line 10837

def self.disease_associated_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001771')
end

.disease_causing_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001772)

# File 'lib/biointerchange/so.rb', line 10843

def self.disease_causing_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001772')
end

.dispersed_repeat ⇒ Object

A repeat that is located at dispersed sites in the genome. (http://purl.obolibrary.org/obo/SO_0000658)

# File 'lib/biointerchange/so.rb', line 4271

def self.dispersed_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000658')
end

.disruptive_inframe_deletion ⇒ Object

An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon. (http://purl.obolibrary.org/obo/SO_0001826)

# File 'lib/biointerchange/so.rb', line 11161

def self.disruptive_inframe_deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001826')
end

.disruptive_inframe_insertion ⇒ Object

An inframe_increase_in_cds_length that inserts one or more codons into the coding sequence within an existing codon. (http://purl.obolibrary.org/obo/SO_0001824)

# File 'lib/biointerchange/so.rb', line 11149

def self.disruptive_inframe_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001824')
end

.distal_duplication ⇒ Object

A duplication of the distal region of a chromosome. (http://purl.obolibrary.org/obo/SO_0001928)

# File 'lib/biointerchange/so.rb', line 11773

def self.distal_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001928')
end

.distal_promoter_element ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001670)

# File 'lib/biointerchange/so.rb', line 10231

def self.distal_promoter_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001670')
end

.distant_three_prime_recoding_signal ⇒ Object

A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon. (http://purl.obolibrary.org/obo/SO_1001287)

# File 'lib/biointerchange/so.rb', line 13655

def self.distant_three_prime_recoding_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001287')
end

.disulfide_bond ⇒ Object

The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules. (http://purl.obolibrary.org/obo/SO_0001088)

# File 'lib/biointerchange/so.rb', line 6799

def self.disulfide_bond
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001088')
end

.DJ_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000539)

# File 'lib/biointerchange/so.rb', line 3553

def self.DJ_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000539')
end

.DJ_gene_segment ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment. (http://purl.obolibrary.org/obo/SO_0000572)

# File 'lib/biointerchange/so.rb', line 3755

def self.DJ_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000572')
end

.DJ_J_C_cluster ⇒ Object

Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE. (http://purl.obolibrary.org/obo/SO_0000540)

# File 'lib/biointerchange/so.rb', line 3559

def self.DJ_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000540')
end

.DJ_J_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene. (http://purl.obolibrary.org/obo/SO_0000485)

# File 'lib/biointerchange/so.rb', line 3229

def self.DJ_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000485')
end

.DMv1_motif ⇒ Object

A promoter motif with consensus sequence CARCCCT. (http://purl.obolibrary.org/obo/SO_0001165)

# File 'lib/biointerchange/so.rb', line 7261

def self.DMv1_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001165')
end

.DMv2_motif ⇒ Object

A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162). (http://purl.obolibrary.org/obo/SO_0001161)

# File 'lib/biointerchange/so.rb', line 7237

def self.DMv2_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001161')
end

.DMv3_motif ⇒ Object

A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162). (http://purl.obolibrary.org/obo/SO_0001160)

# File 'lib/biointerchange/so.rb', line 7231

def self.DMv3_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001160')
end

.DMv4_motif ⇒ Object

A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014). (http://purl.obolibrary.org/obo/SO_0001157)

# File 'lib/biointerchange/so.rb', line 7213

def self.DMv4_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001157')
end

.DMv5_motif ⇒ Object

A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162). (http://purl.obolibrary.org/obo/SO_0001159)

# File 'lib/biointerchange/so.rb', line 7225

def self.DMv5_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001159')
end

.DNA ⇒ Object

An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone. (http://purl.obolibrary.org/obo/SO_0000352)

# File 'lib/biointerchange/so.rb', line 2433

def self.DNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000352')
end

.DNA_aptamer ⇒ Object

DNA molecules that have been selected from random pools based on their ability to bind other molecules. (http://purl.obolibrary.org/obo/SO_0000032)

# File 'lib/biointerchange/so.rb', line 501

def self.DNA_aptamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000032')
end

.DNA_binding_site ⇒ Object

A binding site that, in the molecule, interacts selectively and non-covalently with DNA. (http://purl.obolibrary.org/obo/SO_0001429)

# File 'lib/biointerchange/so.rb', line 8839

def self.DNA_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001429')
end

.DNA_chromosome ⇒ Object

Structural unit composed of a self-replicating, DNA molecule. (http://purl.obolibrary.org/obo/SO_0000954)

# File 'lib/biointerchange/so.rb', line 6005

def self.DNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000954')
end

.DNA_constraint_sequence ⇒ Object

A double-stranded DNA used to control macromolecular structure and function. (http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au]&dispmax=50) (http://purl.obolibrary.org/obo/SO_0001009)

# File 'lib/biointerchange/so.rb', line 6329

def self.DNA_constraint_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001009')
end

.DNA_invertase_target_sequence ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000660)

# File 'lib/biointerchange/so.rb', line 4283

def self.DNA_invertase_target_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000660')
end

.DNA_motif ⇒ Object

A motif that is active in the DNA form of the sequence. (http://purl.obolibrary.org/obo/SO_0000713)

# File 'lib/biointerchange/so.rb', line 4601

def self.DNA_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000713')
end

.DNA_replication_mode ⇒ Object

This has been obsoleted as it represents a process. replaced_by: GO:0006260. (http://purl.obolibrary.org/obo/SO_0000971)

# File 'lib/biointerchange/so.rb', line 6107

def self.DNA_replication_mode
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000971')
end

.DNA_sequence_secondary_structure ⇒ Object

A folded DNA sequence. (http://purl.obolibrary.org/obo/SO_0000142)

# File 'lib/biointerchange/so.rb', line 1169

def self.DNA_sequence_secondary_structure
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000142')
end

.DNA_transposon ⇒ Object

A transposon where the mechanism of transposition is via a DNA intermediate. (http://purl.obolibrary.org/obo/SO_0000182)

# File 'lib/biointerchange/so.rb', line 1413

def self.DNA_transposon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000182')
end

.DNAseI_hypersensitive_site ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000685)

# File 'lib/biointerchange/so.rb', line 4433

def self.DNAseI_hypersensitive_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000685')
end

.DNAzyme ⇒ Object

A DNA sequence with catalytic activity. (http://purl.obolibrary.org/obo/SO_0001012)

# File 'lib/biointerchange/so.rb', line 6347

def self.DNAzyme
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001012')
end

.double ⇒ Object

Attributes added to describe the different kinds of replicon. SO workshop, September 2006. (http://purl.obolibrary.org/obo/SO_0000985)

# File 'lib/biointerchange/so.rb', line 6185

def self.double
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000985')
end

.double_stranded_cDNA ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000758)

# File 'lib/biointerchange/so.rb', line 4871

def self.double_stranded_cDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000758')
end

.double_stranded_DNA_chromosome ⇒ Object

Structural unit composed of a self-replicating, double-stranded DNA molecule. (http://purl.obolibrary.org/obo/SO_0000955)

# File 'lib/biointerchange/so.rb', line 6011

def self.double_stranded_DNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000955')
end

.double_stranded_RNA_chromosome ⇒ Object

Structural unit composed of a self-replicating, double-stranded RNA molecule. (http://purl.obolibrary.org/obo/SO_0000965)

# File 'lib/biointerchange/so.rb', line 6071

def self.double_stranded_RNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000965')
end

.downstream_gene_variant ⇒ Object

A sequence variant located 3' of a gene. (http://purl.obolibrary.org/obo/SO_0001632)

# File 'lib/biointerchange/so.rb', line 10027

def self.downstream_gene_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001632')
end

.downstream_transcript_variant ⇒ Object

Requested by Graham Ritchie, EBI/Sanger. (http://purl.obolibrary.org/obo/SO_0001987)

# File 'lib/biointerchange/so.rb', line 12125

def self.downstream_transcript_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001987')
end

.DPE1_motif ⇒ Object

A promoter motif with consensus sequence CGGACGT. (http://purl.obolibrary.org/obo/SO_0001164)

# File 'lib/biointerchange/so.rb', line 7255

def self.DPE1_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001164')
end

.DPE_motif ⇒ Object

A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C). (http://purl.obolibrary.org/obo/SO_0000015)

# File 'lib/biointerchange/so.rb', line 405

def self.DPE_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000015')
end

.DRE ⇒ Object

A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis. (http://purl.obolibrary.org/obo/SO_0001845)

# File 'lib/biointerchange/so.rb', line 11275

def self.DRE
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001845')
end

.DRE_motif ⇒ Object

A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW. (http://purl.obolibrary.org/obo/SO_0001156)

# File 'lib/biointerchange/so.rb', line 7207

def self.DRE_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001156')
end

.ds_DNA_viral_sequence ⇒ Object

A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA. (http://purl.obolibrary.org/obo/SO_0001198)

# File 'lib/biointerchange/so.rb', line 7459

def self.ds_DNA_viral_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001198')
end

.ds_oligo ⇒ Object

A double stranded oligonucleotide. (http://purl.obolibrary.org/obo/SO_0000442)

# File 'lib/biointerchange/so.rb', line 2971

def self.ds_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000442')
end

.ds_RNA_viral_sequence ⇒ Object

A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA. (http://purl.obolibrary.org/obo/SO_0001169)

# File 'lib/biointerchange/so.rb', line 7285

def self.ds_RNA_viral_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001169')
end

.DSR_motif ⇒ Object

The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome. (http://purl.obolibrary.org/obo/SO_0002005)

# File 'lib/biointerchange/so.rb', line 12233

def self.DSR_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002005')
end

.DsrA_RNA ⇒ Object

DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation. (http://purl.obolibrary.org/obo/SO_0000378)

# File 'lib/biointerchange/so.rb', line 2583

def self.DsrA_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000378')
end

.duplicated_pseudogene ⇒ Object

A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence. (http://purl.obolibrary.org/obo/SO_0001758)

# File 'lib/biointerchange/so.rb', line 10759

def self.duplicated_pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001758')
end

.duplication ⇒ Object

An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome. (http://purl.obolibrary.org/obo/SO_1000035)

# File 'lib/biointerchange/so.rb', line 12641

def self.duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000035')
end

.duplication_attribute ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001523)

# File 'lib/biointerchange/so.rb', line 9397

def self.duplication_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001523')
end

.dye_terminator_read ⇒ Object

A read produced by the dye terminator method of sequencing. (http://purl.obolibrary.org/obo/SO_0001423)

# File 'lib/biointerchange/so.rb', line 8803

def self.dye_terminator_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001423')
end

.E_box_motif ⇒ Object

A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015). (http://purl.obolibrary.org/obo/SO_0001158)

# File 'lib/biointerchange/so.rb', line 7219

def self.E_box_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001158')
end

.edit_operation ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000916)

# File 'lib/biointerchange/so.rb', line 5777

def self.edit_operation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000916')
end

.edited ⇒ Object

An attribute describing a sequence that is modified by editing. (http://purl.obolibrary.org/obo/SO_0000116)

# File 'lib/biointerchange/so.rb', line 1013

def self.edited
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000116')
end

.edited_by_A_to_I_substitution ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000600)

# File 'lib/biointerchange/so.rb', line 3923

def self.edited_by_A_to_I_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000600')
end

.edited_by_C_insertion_and_dinucleotide_insertion ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000598)

# File 'lib/biointerchange/so.rb', line 3911

def self.edited_by_C_insertion_and_dinucleotide_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000598')
end

.edited_by_C_to_U_substitution ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000599)

# File 'lib/biointerchange/so.rb', line 3917

def self.edited_by_C_to_U_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000599')
end

.edited_by_G_addition ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000601)

# File 'lib/biointerchange/so.rb', line 3929

def self.edited_by_G_addition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000601')
end

.edited_CDS ⇒ Object

A CDS that is edited. (http://purl.obolibrary.org/obo/SO_0000935)

# File 'lib/biointerchange/so.rb', line 5891

def self.edited_CDS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000935')
end

.edited_from ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#edited_from)

# File 'lib/biointerchange/so.rb', line 65

def self.edited_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#edited_from')
end

.edited_mRNA ⇒ Object

An mRNA that is edited. (http://purl.obolibrary.org/obo/SO_0000929)

# File 'lib/biointerchange/so.rb', line 5855

def self.edited_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000929')
end

.edited_to ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#edited_to)

# File 'lib/biointerchange/so.rb', line 71

def self.edited_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#edited_to')
end

.edited_transcript ⇒ Object

A transcript that is edited. (http://purl.obolibrary.org/obo/SO_0000873)

# File 'lib/biointerchange/so.rb', line 5519

def self.edited_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000873')
end

.edited_transcript_by_A_to_I_substitution ⇒ Object

A transcript that has been edited by A to I substitution. (http://purl.obolibrary.org/obo/SO_0000874)

# File 'lib/biointerchange/so.rb', line 5525

def self.edited_transcript_by_A_to_I_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000874')
end

.edited_transcript_feature ⇒ Object

A locatable feature on a transcript that is edited. (http://purl.obolibrary.org/obo/SO_0000579)

# File 'lib/biointerchange/so.rb', line 3797

def self.edited_transcript_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000579')
end

.editing_block ⇒ Object

Edited mRNA sequence mediated by a single guide RNA (SO:0000602). (http://purl.obolibrary.org/obo/SO_0000604)

# File 'lib/biointerchange/so.rb', line 3947

def self.editing_block
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000604')
end

.editing_domain ⇒ Object

Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602). (http://purl.obolibrary.org/obo/SO_0000606)

# File 'lib/biointerchange/so.rb', line 3959

def self.editing_domain
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000606')
end

.editing_variant ⇒ Object

A transcript processing variant whereby the process of editing is disrupted with respect to the reference. (http://purl.obolibrary.org/obo/SO_0001544)

# File 'lib/biointerchange/so.rb', line 9523

def self.editing_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001544')
end

.eight_cutter_restriction_site ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000251)

# File 'lib/biointerchange/so.rb', line 1827

def self.eight_cutter_restriction_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000251')
end

.elongated_in_frame_polypeptide_C_terminal ⇒ Object

A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus. (http://purl.obolibrary.org/obo/SO_0001612)

# File 'lib/biointerchange/so.rb', line 9913

def self.elongated_in_frame_polypeptide_C_terminal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001612')
end

.elongated_in_frame_polypeptide_N_terminal_elongation ⇒ Object

A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus. (http://purl.obolibrary.org/obo/SO_0001614)

# File 'lib/biointerchange/so.rb', line 9925

def self.elongated_in_frame_polypeptide_N_terminal_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001614')
end

.elongated_out_of_frame_polypeptide_C_terminal ⇒ Object

A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus. (http://purl.obolibrary.org/obo/SO_0001613)

# File 'lib/biointerchange/so.rb', line 9919

def self.elongated_out_of_frame_polypeptide_C_terminal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001613')
end

.elongated_out_of_frame_polypeptide_N_terminal ⇒ Object

A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus. (http://purl.obolibrary.org/obo/SO_0001615)

# File 'lib/biointerchange/so.rb', line 9931

def self.elongated_out_of_frame_polypeptide_N_terminal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001615')
end

.elongated_polypeptide ⇒ Object

A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence. (http://purl.obolibrary.org/obo/SO_0001609)

# File 'lib/biointerchange/so.rb', line 9895

def self.elongated_polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001609')
end

.elongated_polypeptide_C_terminal ⇒ Object

A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus. (http://purl.obolibrary.org/obo/SO_0001610)

# File 'lib/biointerchange/so.rb', line 9901

def self.elongated_polypeptide_C_terminal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001610')
end

.elongated_polypeptide_N_terminal ⇒ Object

A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus. (http://purl.obolibrary.org/obo/SO_0001611)

# File 'lib/biointerchange/so.rb', line 9907

def self.elongated_polypeptide_N_terminal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001611')
end

.encodes_1_polypeptide ⇒ Object

A gene that is alternately spliced, but encodes only one polypeptide. (http://purl.obolibrary.org/obo/SO_1001188)

# File 'lib/biointerchange/so.rb', line 13391

def self.encodes_1_polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001188')
end

.encodes_alternate_transcription_start_sites ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001241)

# File 'lib/biointerchange/so.rb', line 7717

def self.encodes_alternate_transcription_start_sites
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001241')
end

.encodes_alternately_spliced_transcripts ⇒ Object

A gene that encodes more than one transcript. (http://purl.obolibrary.org/obo/SO_0000463)

# File 'lib/biointerchange/so.rb', line 3097

def self.encodes_alternately_spliced_transcripts
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000463')
end

.encodes_different_polypeptides_different_stop ⇒ Object

A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons. (http://purl.obolibrary.org/obo/SO_1001190)

# File 'lib/biointerchange/so.rb', line 13403

def self.encodes_different_polypeptides_different_stop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001190')
end

.encodes_disjoint_polypeptides ⇒ Object

A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences. (http://purl.obolibrary.org/obo/SO_1001192)

# File 'lib/biointerchange/so.rb', line 13415

def self.encodes_disjoint_polypeptides
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001192')
end

.encodes_greater_than_1_polypeptide ⇒ Object

A gene that is alternately spliced, and encodes more than one polypeptide. (http://purl.obolibrary.org/obo/SO_1001189)

# File 'lib/biointerchange/so.rb', line 13397

def self.encodes_greater_than_1_polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001189')
end

.encodes_overlapping_peptides ⇒ Object

A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences. (http://purl.obolibrary.org/obo/SO_1001195)

# File 'lib/biointerchange/so.rb', line 13433

def self.encodes_overlapping_peptides
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001195')
end

.encodes_overlapping_peptides_different_start ⇒ Object

A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons. (http://purl.obolibrary.org/obo/SO_1001191)

# File 'lib/biointerchange/so.rb', line 13409

def self.encodes_overlapping_peptides_different_start
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001191')
end

.encodes_overlapping_polypeptides_different_start_and_stop ⇒ Object

A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons. (http://purl.obolibrary.org/obo/SO_1001193)

# File 'lib/biointerchange/so.rb', line 13421

def self.encodes_overlapping_polypeptides_different_start_and_stop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001193')
end

.end_overlapping_gene ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000072)

# File 'lib/biointerchange/so.rb', line 749

def self.end_overlapping_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000072')
end

.endogenous_retroviral_gene ⇒ Object

A proviral gene with origin endogenous retrovirus. (http://purl.obolibrary.org/obo/SO_0000100)

# File 'lib/biointerchange/so.rb', line 917

def self.endogenous_retroviral_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000100')
end

.endogenous_retroviral_sequence ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000903)

# File 'lib/biointerchange/so.rb', line 5699

def self.endogenous_retroviral_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000903')
end

.endonuclease_spliced_intron ⇒ Object

An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification. (http://purl.obolibrary.org/obo/SO_0001216)

# File 'lib/biointerchange/so.rb', line 7567

def self.endonuclease_spliced_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001216')
end

.endosomal_localization_signal ⇒ Object

A polypeptide region that targets a polypeptide to the endosome. (http://purl.obolibrary.org/obo/SO_0001529)

# File 'lib/biointerchange/so.rb', line 9433

def self.endosomal_localization_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001529')
end

.engineered ⇒ Object

An attribute to describe a region that was modified in vitro. (http://purl.obolibrary.org/obo/SO_0000783)

# File 'lib/biointerchange/so.rb', line 5015

def self.engineered
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000783')
end

.engineered_DNA ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000793)

# File 'lib/biointerchange/so.rb', line 5075

def self.engineered_DNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000793')
end

.engineered_episome ⇒ Object

An episome that is engineered. (http://purl.obolibrary.org/obo/SO_0000779)

# File 'lib/biointerchange/so.rb', line 4991

def self.engineered_episome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000779')
end

.engineered_foreign_gene ⇒ Object

A gene that is engineered and foreign. (http://purl.obolibrary.org/obo/SO_0000281)

# File 'lib/biointerchange/so.rb', line 2007

def self.engineered_foreign_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000281')
end

.engineered_foreign_region ⇒ Object

A region that is engineered and foreign. (http://purl.obolibrary.org/obo/SO_0000805)

# File 'lib/biointerchange/so.rb', line 5123

def self.engineered_foreign_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000805')
end

.engineered_foreign_repetitive_element ⇒ Object

A repetitive element that is engineered and foreign. (http://purl.obolibrary.org/obo/SO_0000293)

# File 'lib/biointerchange/so.rb', line 2079

def self.engineered_foreign_repetitive_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000293')
end

.engineered_foreign_transposable_element ⇒ Object

A transposable_element that is engineered and foreign. (http://purl.obolibrary.org/obo/SO_0000799)

# File 'lib/biointerchange/so.rb', line 5111

def self.engineered_foreign_transposable_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000799')
end

.engineered_foreign_transposable_element_gene ⇒ Object

A transposable_element that is engineered and foreign. (http://purl.obolibrary.org/obo/SO_0000283)

# File 'lib/biointerchange/so.rb', line 2019

def self.engineered_foreign_transposable_element_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000283')
end

.engineered_fusion_gene ⇒ Object

A fusion gene that is engineered. (http://purl.obolibrary.org/obo/SO_0000288)

# File 'lib/biointerchange/so.rb', line 2049

def self.engineered_fusion_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000288')
end

.engineered_gene ⇒ Object

A gene that is engineered. (http://purl.obolibrary.org/obo/SO_0000280)

# File 'lib/biointerchange/so.rb', line 2001

def self.engineered_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000280')
end

.engineered_insert ⇒ Object

A clone insert that is engineered. (http://purl.obolibrary.org/obo/SO_0000915)

# File 'lib/biointerchange/so.rb', line 5771

def self.engineered_insert
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000915')
end

.engineered_plasmid ⇒ Object

A plasmid that is engineered. (http://purl.obolibrary.org/obo/SO_0000637)

# File 'lib/biointerchange/so.rb', line 4145

def self.engineered_plasmid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000637')
end

.engineered_region ⇒ Object

A region that is engineered. (http://purl.obolibrary.org/obo/SO_0000804)

# File 'lib/biointerchange/so.rb', line 5117

def self.engineered_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000804')
end

.engineered_rescue_region ⇒ Object

A rescue region that is engineered. (http://purl.obolibrary.org/obo/SO_0000794)

# File 'lib/biointerchange/so.rb', line 5081

def self.engineered_rescue_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000794')
end

.engineered_tag ⇒ Object

A tag that is engineered. (http://purl.obolibrary.org/obo/SO_0000807)

# File 'lib/biointerchange/so.rb', line 5135

def self.engineered_tag
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000807')
end

.engineered_transposable_element ⇒ Object

TE that has been modified by manipulations in vitro. (http://purl.obolibrary.org/obo/SO_0000798)

# File 'lib/biointerchange/so.rb', line 5105

def self.engineered_transposable_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000798')
end

.enhanceosome ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001057)

# File 'lib/biointerchange/so.rb', line 6625

def self.enhanceosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001057')
end

.enhancer ⇒ Object

A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. (http://purl.obolibrary.org/obo/SO_0000165)

# File 'lib/biointerchange/so.rb', line 1307

def self.enhancer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000165')
end

.enhancer_attribute ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000402)

# File 'lib/biointerchange/so.rb', line 2727

def self.enhancer_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000402')
end

.enhancer_binding_site ⇒ Object

A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. (http://purl.obolibrary.org/obo/SO_0001461)

# File 'lib/biointerchange/so.rb', line 9025

def self.enhancer_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001461')
end

.enhancer_bound_by_factor ⇒ Object

An enhancer bound by a factor. (http://purl.obolibrary.org/obo/SO_0000166)

# File 'lib/biointerchange/so.rb', line 1313

def self.enhancer_bound_by_factor
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000166')
end

.enhancer_trap_construct ⇒ Object

An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic. (http://purl.obolibrary.org/obo/SO_0001479)

# File 'lib/biointerchange/so.rb', line 9133

def self.enhancer_trap_construct
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001479')
end

.enhancerRNA ⇒ Object

A short ncRNA that is transcribed from an enhancer. May have a regulatory function. (http://purl.obolibrary.org/obo/SO_0001870)

# File 'lib/biointerchange/so.rb', line 11425

def self.enhancerRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001870')
end

.enzymatic ⇒ Object

An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein. (http://purl.obolibrary.org/obo/SO_0001185)

# File 'lib/biointerchange/so.rb', line 7381

def self.enzymatic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001185')
end

.enzymatic_RNA ⇒ Object

An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein. (http://purl.obolibrary.org/obo/SO_0000372)

# File 'lib/biointerchange/so.rb', line 2547

def self.enzymatic_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000372')
end

.epigenetically_modified ⇒ Object

This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones. (http://purl.obolibrary.org/obo/SO_0000133)

# File 'lib/biointerchange/so.rb', line 1115

def self.epigenetically_modified
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000133')
end

.epigenetically_modified_gene ⇒ Object

A gene that is epigenetically modified. (http://purl.obolibrary.org/obo/SO_0000898)

# File 'lib/biointerchange/so.rb', line 5669

def self.epigenetically_modified_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000898')
end

.epigenetically_modified_region ⇒ Object

A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence. (http://purl.obolibrary.org/obo/SO_0001720)

# File 'lib/biointerchange/so.rb', line 10531

def self.epigenetically_modified_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001720')
end

.episome ⇒ Object

A plasmid that may integrate with a chromosome. (http://purl.obolibrary.org/obo/SO_0000768)

# File 'lib/biointerchange/so.rb', line 4925

def self.episome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000768')
end

.epitope ⇒ Object

A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells. (http://purl.obolibrary.org/obo/SO_0001018)

# File 'lib/biointerchange/so.rb', line 6383

def self.epitope
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001018')
end

.epoxyqueuosine ⇒ Object

Epoxyqueuosine is a modified 7-deazoguanosine. (http://purl.obolibrary.org/obo/SO_0001318)

# File 'lib/biointerchange/so.rb', line 8173

def self.epoxyqueuosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001318')
end

.ER_retention_signal ⇒ Object

A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL. (http://purl.obolibrary.org/obo/SO_0001806)

# File 'lib/biointerchange/so.rb', line 11041

def self.ER_retention_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001806')
end

.EST ⇒ Object

A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long. (http://purl.obolibrary.org/obo/SO_0000345)

# File 'lib/biointerchange/so.rb', line 2391

def self.EST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000345')
end

.EST_match ⇒ Object

A match against an EST sequence. (http://purl.obolibrary.org/obo/SO_0000668)

# File 'lib/biointerchange/so.rb', line 4331

def self.EST_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000668')
end

.eukaryotic_terminator ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000951)

# File 'lib/biointerchange/so.rb', line 5987

def self.eukaryotic_terminator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000951')
end

.evidence_for_feature ⇒ Object

B is evidence_for_feature A, if an instance of B supports the existence of A. (http://purl.obolibrary.org/obo/so_2_5_2.obo#evidence_for_feature)

# File 'lib/biointerchange/so.rb', line 77

def self.evidence_for_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#evidence_for_feature')
end

.exemplar ⇒ Object

An attribute describing a sequence is representative of a class of similar sequences. (http://purl.obolibrary.org/obo/SO_0000864)

# File 'lib/biointerchange/so.rb', line 5465

def self.exemplar
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000864')
end

.exemplar_mRNA ⇒ Object

An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group. (http://purl.obolibrary.org/obo/SO_0000734)

# File 'lib/biointerchange/so.rb', line 4727

def self.exemplar_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000734')
end

.exemplar_of ⇒ Object

X is exemplar of Y if X is the best evidence for Y. (http://purl.obolibrary.org/obo/so_2_5_2.obo#exemplar_of)

# File 'lib/biointerchange/so.rb', line 83

def self.exemplar_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#exemplar_of')
end

.exon ⇒ Object

A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. (http://purl.obolibrary.org/obo/SO_0000147)

# File 'lib/biointerchange/so.rb', line 1199

def self.exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000147')
end

.exon_junction ⇒ Object

The boundary between two exons in a processed transcript. (http://purl.obolibrary.org/obo/SO_0000333)

# File 'lib/biointerchange/so.rb', line 2319

def self.exon_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000333')
end

.exon_loss_variant ⇒ Object

A sequence variant whereby an exon is lost from the transcript. (http://purl.obolibrary.org/obo/SO_0001572)

# File 'lib/biointerchange/so.rb', line 9691

def self.exon_loss_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001572')
end

.exon_of_single_exon_gene ⇒ Object

An exon that is the only exon in a gene. (http://purl.obolibrary.org/obo/SO_0005845)

# File 'lib/biointerchange/so.rb', line 12275

def self.exon_of_single_exon_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005845')
end

.exon_region ⇒ Object

A region of an exon. (http://purl.obolibrary.org/obo/SO_0000852)

# File 'lib/biointerchange/so.rb', line 5393

def self.exon_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000852')
end

.exon_variant ⇒ Object

A sequence variant that changes exon sequence. (http://purl.obolibrary.org/obo/SO_0001791)

# File 'lib/biointerchange/so.rb', line 10951

def self.exon_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001791')
end

.exonic_splice_enhancer ⇒ Object

Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron. (http://purl.obolibrary.org/obo/SO_0000683)

# File 'lib/biointerchange/so.rb', line 4421

def self.exonic_splice_enhancer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000683')
end

.experimental_feature ⇒ Object

A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. (http://purl.obolibrary.org/obo/SO_0001410)

# File 'lib/biointerchange/so.rb', line 8725

def self.experimental_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001410')
end

.experimental_feature_attribute ⇒ Object

An attribute of an experimentally derived feature. (http://purl.obolibrary.org/obo/SO_0001684)

# File 'lib/biointerchange/so.rb', line 10315

def self.experimental_feature_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001684')
end

.experimental_result_region ⇒ Object

A region of sequence implicated in an experimental result. (http://purl.obolibrary.org/obo/SO_0000703)

# File 'lib/biointerchange/so.rb', line 4541

def self.experimental_result_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000703')
end

.experimentally_defined_binding_region ⇒ Object

A region that has been implicated in binding although the exact coordinates of binding may be unknown. (http://purl.obolibrary.org/obo/SO_0001696)

# File 'lib/biointerchange/so.rb', line 10387

def self.experimentally_defined_binding_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001696')
end

.experimentally_determined ⇒ Object

Attribute to describe a feature that has been experimentally verified. (http://purl.obolibrary.org/obo/SO_0000312)

# File 'lib/biointerchange/so.rb', line 2193

def self.experimentally_determined
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000312')
end

.expressed_sequence_assembly ⇒ Object

A sequence assembly derived from expressed sequences. (http://purl.obolibrary.org/obo/SO_0001428)

# File 'lib/biointerchange/so.rb', line 8833

def self.expressed_sequence_assembly
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001428')
end

.expressed_sequence_match ⇒ Object

A match to an EST or cDNA sequence. (http://purl.obolibrary.org/obo/SO_0000102)

# File 'lib/biointerchange/so.rb', line 929

def self.expressed_sequence_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000102')
end

.extended_cis_splice_site ⇒ Object

Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after. (http://purl.obolibrary.org/obo/SO_0001993)

# File 'lib/biointerchange/so.rb', line 12161

def self.extended_cis_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001993')
end

.extended_intronic_splice_region ⇒ Object

Region of intronic sequence within 10 bases of an exon. (http://purl.obolibrary.org/obo/SO_0001996)

# File 'lib/biointerchange/so.rb', line 12179

def self.extended_intronic_splice_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001996')
end

.extended_intronic_splice_region_variant ⇒ Object

A sequence variant occurring in the intron, within 10 bases of exon. (http://purl.obolibrary.org/obo/SO_0001995)

# File 'lib/biointerchange/so.rb', line 12173

def self.extended_intronic_splice_region_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001995')
end

.external_transcribed_spacer_region ⇒ Object

Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA. (http://purl.obolibrary.org/obo/SO_0000640)

# File 'lib/biointerchange/so.rb', line 4163

def self.external_transcribed_spacer_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000640')
end

.extrachromosomal_mobile_genetic_element ⇒ Object

An MGE that is not integrated into the host chromosome. (http://purl.obolibrary.org/obo/SO_0001038)

# File 'lib/biointerchange/so.rb', line 6503

def self.extrachromosomal_mobile_genetic_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001038')
end

.extramembrane_polypeptide_region ⇒ Object

Polypeptide region that is localized outside of a lipid bilayer. (http://purl.obolibrary.org/obo/SO_0001072)

# File 'lib/biointerchange/so.rb', line 6703

def self.extramembrane_polypeptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001072')
end

.feature_ablation ⇒ Object

A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features. (http://purl.obolibrary.org/obo/SO_0001879)

# File 'lib/biointerchange/so.rb', line 11479

def self.feature_ablation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001879')
end

.feature_amplification ⇒ Object

A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features. (http://purl.obolibrary.org/obo/SO_0001880)

# File 'lib/biointerchange/so.rb', line 11485

def self.feature_amplification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001880')
end

.feature_attribute ⇒ Object

An attribute describing a located_sequence_feature. (http://purl.obolibrary.org/obo/SO_0000733)

# File 'lib/biointerchange/so.rb', line 4721

def self.feature_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000733')
end

.feature_elongation ⇒ Object

A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence. (http://purl.obolibrary.org/obo/SO_0001907)

# File 'lib/biointerchange/so.rb', line 11647

def self.feature_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001907')
end

.feature_fusion ⇒ Object

A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features. (http://purl.obolibrary.org/obo/SO_0001882)

# File 'lib/biointerchange/so.rb', line 11497

def self.feature_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001882')
end

.feature_translocation ⇒ Object

A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features. (http://purl.obolibrary.org/obo/SO_0001881)

# File 'lib/biointerchange/so.rb', line 11491

def self.feature_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001881')
end

.feature_truncation ⇒ Object

A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence. (http://purl.obolibrary.org/obo/SO_0001906)

# File 'lib/biointerchange/so.rb', line 11641

def self.feature_truncation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001906')
end

.feature_variant ⇒ Object

A sequence variant that falls entirely or partially within a genomic feature. (http://purl.obolibrary.org/obo/SO_0001878)

# File 'lib/biointerchange/so.rb', line 11473

def self.feature_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001878')
end

.fingerprint_map ⇒ Object

A fingerprint_map is a physical map composed of restriction fragments. (http://purl.obolibrary.org/obo/SO_0001250)

# File 'lib/biointerchange/so.rb', line 7765

def self.fingerprint_map
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001250')
end

.finished_by ⇒ Object

Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary. (http://purl.obolibrary.org/obo/so_2_5_2.obo#finished_by)

# File 'lib/biointerchange/so.rb', line 89

def self.finished_by
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#finished_by')
end

.finished_genome ⇒ Object

The status of a whole genome sequence, with less than 1 error per 100,000 base pairs. (http://purl.obolibrary.org/obo/SO_0001491)

# File 'lib/biointerchange/so.rb', line 9205

def self.finished_genome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001491')
end

.finishes ⇒ Object

X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary. (http://purl.obolibrary.org/obo/so_2_5_2.obo#finishes)

# File 'lib/biointerchange/so.rb', line 95

def self.finishes
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#finishes')
end

.five_aminomethyl_two_thiouridine ⇒ Object

5_aminomethyl_2_thiouridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001363)

# File 'lib/biointerchange/so.rb', line 8443

def self.five_aminomethyl_two_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001363')
end

.five_carbamoylmethyl_two_prime_O_methyluridine ⇒ Object

5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001368)

# File 'lib/biointerchange/so.rb', line 8473

def self.five_carbamoylmethyl_two_prime_O_methyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001368')
end

.five_carbamoylmethyluridine ⇒ Object

5_carbamoylmethyluridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001367)

# File 'lib/biointerchange/so.rb', line 8467

def self.five_carbamoylmethyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001367')
end

.five_carboxyhydroxymethyl_uridine ⇒ Object

5_carboxyhydroxymethyl_uridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001358)

# File 'lib/biointerchange/so.rb', line 8413

def self.five_carboxyhydroxymethyl_uridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001358')
end

.five_carboxyhydroxymethyl_uridine_methyl_ester ⇒ Object

5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001359)

# File 'lib/biointerchange/so.rb', line 8419

def self.five_carboxyhydroxymethyl_uridine_methyl_ester
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001359')
end

.five_carboxymethylaminomethyl_two_prime_O_methyluridine ⇒ Object

5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001370)

# File 'lib/biointerchange/so.rb', line 8485

def self.five_carboxymethylaminomethyl_two_prime_O_methyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001370')
end

.five_carboxymethylaminomethyl_two_thiouridine ⇒ Object

5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001371)

# File 'lib/biointerchange/so.rb', line 8491

def self.five_carboxymethylaminomethyl_two_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001371')
end

.five_carboxymethylaminomethyluridine ⇒ Object

5_carboxymethylaminomethyluridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001369)

# File 'lib/biointerchange/so.rb', line 8479

def self.five_carboxymethylaminomethyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001369')
end

.five_carboxymethyluridine ⇒ Object

5_carboxymethyluridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001374)

# File 'lib/biointerchange/so.rb', line 8509

def self.five_carboxymethyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001374')
end

.five_formyl_two_prime_O_methylcytidine ⇒ Object

5-formyl-2'-O-methylcytidine is a modified cytidine. (http://purl.obolibrary.org/obo/SO_0001293)

# File 'lib/biointerchange/so.rb', line 8023

def self.five_formyl_two_prime_O_methylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001293')
end

.five_formylcytidine ⇒ Object

5-formylcytidine is a modified cytidine. (http://purl.obolibrary.org/obo/SO_0001286)

# File 'lib/biointerchange/so.rb', line 7981

def self.five_formylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001286')
end

.five_hydroxymethylcytidine ⇒ Object

5-hydroxymethylcytidine is a modified cytidine. (http://purl.obolibrary.org/obo/SO_0001292)

# File 'lib/biointerchange/so.rb', line 8017

def self.five_hydroxymethylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001292')
end

.five_hydroxyuridine ⇒ Object

5_hydroxyuridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001354)

# File 'lib/biointerchange/so.rb', line 8389

def self.five_hydroxyuridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001354')
end

.five_isopentenylaminomethyl_two_prime_O_methyluridine ⇒ Object

5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001382)

# File 'lib/biointerchange/so.rb', line 8557

def self.five_isopentenylaminomethyl_two_prime_O_methyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001382')
end

.five_isopentenylaminomethyl_two_thiouridine ⇒ Object

5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001381)

# File 'lib/biointerchange/so.rb', line 8551

def self.five_isopentenylaminomethyl_two_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001381')
end

.five_isopentenylaminomethyl_uridine ⇒ Object

5_isopentenylaminomethyl_uridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001380)

# File 'lib/biointerchange/so.rb', line 8545

def self.five_isopentenylaminomethyl_uridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001380')
end

.five_methoxycarbonylmethyl_two_prime_O_methyluridine ⇒ Object

Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001361)

# File 'lib/biointerchange/so.rb', line 8431

def self.five_methoxycarbonylmethyl_two_prime_O_methyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001361')
end

.five_methoxycarbonylmethyl_two_thiouridine ⇒ Object

5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001362)

# File 'lib/biointerchange/so.rb', line 8437

def self.five_methoxycarbonylmethyl_two_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001362')
end

.five_methoxycarbonylmethyluridine ⇒ Object

Five_methoxycarbonylmethyluridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001360)

# File 'lib/biointerchange/so.rb', line 8425

def self.five_methoxycarbonylmethyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001360')
end

.five_methoxyuridine ⇒ Object

5_methoxyuridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001355)

# File 'lib/biointerchange/so.rb', line 8395

def self.five_methoxyuridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001355')
end

.five_methyl_2_thiouridine ⇒ Object

5_methyl_2_thiouridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001351)

# File 'lib/biointerchange/so.rb', line 8371

def self.five_methyl_2_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001351')
end

.five_methylaminomethyl_two_selenouridine ⇒ Object

5_methylaminomethyl_2_selenouridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001366)

# File 'lib/biointerchange/so.rb', line 8461

def self.five_methylaminomethyl_two_selenouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001366')
end

.five_methylaminomethyl_two_thiouridine ⇒ Object

5_methylaminomethyl_2_thiouridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001365)

# File 'lib/biointerchange/so.rb', line 8455

def self.five_methylaminomethyl_two_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001365')
end

.five_methylaminomethyluridine ⇒ Object

5_methylaminomethyluridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001364)

# File 'lib/biointerchange/so.rb', line 8449

def self.five_methylaminomethyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001364')
end

.five_methylcytidine ⇒ Object

5-methylcytidine is a modified cytidine. (http://purl.obolibrary.org/obo/SO_0001282)

# File 'lib/biointerchange/so.rb', line 7957

def self.five_methylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001282')
end

.five_methyldihydrouridine ⇒ Object

5_methyldihydrouridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001376)

# File 'lib/biointerchange/so.rb', line 8521

def self.five_methyldihydrouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001376')
end

.five_methyluridine ⇒ Object

5_methyluridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001344)

# File 'lib/biointerchange/so.rb', line 8329

def self.five_methyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001344')
end

.five_prime_cis_splice_site ⇒ Object

Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron. (http://purl.obolibrary.org/obo/SO_0000163)

# File 'lib/biointerchange/so.rb', line 1295

def self.five_prime_cis_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000163')
end

.five_prime_clip ⇒ Object

5' most region of a precursor transcript that is clipped off during processing. (http://purl.obolibrary.org/obo/SO_0000555)

# File 'lib/biointerchange/so.rb', line 3653

def self.five_prime_clip
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000555')
end

.five_prime_coding_exon ⇒ Object

The 5' most coding exon. (http://purl.obolibrary.org/obo/SO_0000200)

# File 'lib/biointerchange/so.rb', line 1521

def self.five_prime_coding_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000200')
end

.five_prime_coding_exon_coding_region ⇒ Object

The sequence of the five_prime_coding_exon that codes for protein. (http://purl.obolibrary.org/obo/SO_0000196)

# File 'lib/biointerchange/so.rb', line 1497

def self.five_prime_coding_exon_coding_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000196')
end

.five_prime_coding_exon_noncoding_region ⇒ Object

The sequence of the 5' exon preceding the start codon. (http://purl.obolibrary.org/obo/SO_0000486)

# File 'lib/biointerchange/so.rb', line 3235

def self.five_prime_coding_exon_noncoding_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000486')
end

.five_prime_D_heptamer ⇒ Object

7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. (http://purl.obolibrary.org/obo/SO_0000496)

# File 'lib/biointerchange/so.rb', line 3295

def self.five_prime_D_heptamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000496')
end

.five_prime_D_nonamer ⇒ Object

9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. (http://purl.obolibrary.org/obo/SO_0000497)

# File 'lib/biointerchange/so.rb', line 3301

def self.five_prime_D_nonamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000497')
end

.five_prime_D_recombination_signal_sequence ⇒ Object

Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene. (http://purl.obolibrary.org/obo/SO_0000556)

# File 'lib/biointerchange/so.rb', line 3659

def self.five_prime_D_recombination_signal_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000556')
end

.five_prime_D_spacer ⇒ Object

12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. (http://purl.obolibrary.org/obo/SO_0000498)

# File 'lib/biointerchange/so.rb', line 3307

def self.five_prime_D_spacer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000498')
end

.five_prime_EST ⇒ Object

An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family. (http://purl.obolibrary.org/obo/SO_0001208)

# File 'lib/biointerchange/so.rb', line 7519

def self.five_prime_EST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001208')
end

.five_prime_five_prime_overlap ⇒ Object

An attribute to describe a gene when the five prime region overlaps with another gene's five prime region. (http://purl.obolibrary.org/obo/SO_0000074)

# File 'lib/biointerchange/so.rb', line 761

def self.five_prime_five_prime_overlap
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000074')
end

.five_prime_flanking_region ⇒ Object

A flanking region located five prime of a specific region. (http://purl.obolibrary.org/obo/SO_0001416)

# File 'lib/biointerchange/so.rb', line 8761

def self.five_prime_flanking_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001416')
end

.five_prime_intron ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000190)

# File 'lib/biointerchange/so.rb', line 1461

def self.five_prime_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000190')
end

.five_prime_LTR ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000425)

# File 'lib/biointerchange/so.rb', line 2865

def self.five_prime_LTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000425')
end

.five_prime_LTR_component ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000850)

# File 'lib/biointerchange/so.rb', line 5381

def self.five_prime_LTR_component
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000850')
end

.five_prime_noncoding_exon ⇒ Object

Non-coding exon in the 5' UTR. (http://purl.obolibrary.org/obo/SO_0000445)

# File 'lib/biointerchange/so.rb', line 2989

def self.five_prime_noncoding_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000445')
end

.five_prime_open_reading_frame ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000629)

# File 'lib/biointerchange/so.rb', line 4097

def self.five_prime_open_reading_frame
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000629')
end

.five_prime_recoding_site ⇒ Object

The recoding stimulatory signal located upstream of the recoding site. (http://purl.obolibrary.org/obo/SO_1001280)

# File 'lib/biointerchange/so.rb', line 13613

def self.five_prime_recoding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001280')
end

.five_prime_restriction_enzyme_junction ⇒ Object

The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence. (http://purl.obolibrary.org/obo/SO_0001689)

# File 'lib/biointerchange/so.rb', line 10345

def self.five_prime_restriction_enzyme_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001689')
end

.five_prime_RST ⇒ Object

A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long. (http://purl.obolibrary.org/obo/SO_0001469)

# File 'lib/biointerchange/so.rb', line 9073

def self.five_prime_RST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001469')
end

.five_prime_sticky_end_restriction_enzyme_cleavage_site ⇒ Object

A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs. (http://purl.obolibrary.org/obo/SO_0001975)

# File 'lib/biointerchange/so.rb', line 12059

def self.five_prime_sticky_end_restriction_enzyme_cleavage_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001975')
end

.five_prime_terminal_inverted_repeat ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000420)

# File 'lib/biointerchange/so.rb', line 2835

def self.five_prime_terminal_inverted_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000420')
end

.five_prime_three_prime_overlap ⇒ Object

An attribute to describe a gene when the five prime region overlaps with another gene's 3' region. (http://purl.obolibrary.org/obo/SO_0000073)

# File 'lib/biointerchange/so.rb', line 755

def self.five_prime_three_prime_overlap
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000073')
end

.five_prime_UST ⇒ Object

An UST located in the 5'UTR of a protein-coding transcript. (http://purl.obolibrary.org/obo/SO_0001466)

# File 'lib/biointerchange/so.rb', line 9055

def self.five_prime_UST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001466')
end

.five_prime_UTR ⇒ Object

A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein. (http://purl.obolibrary.org/obo/SO_0000204)

# File 'lib/biointerchange/so.rb', line 1545

def self.five_prime_UTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000204')
end

.five_prime_UTR_intron ⇒ Object

An intron located in the 5' UTR. (http://purl.obolibrary.org/obo/SO_0000447)

# File 'lib/biointerchange/so.rb', line 3001

def self.five_prime_UTR_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000447')
end

.five_prime_UTR_premature_start_codon_location_variant ⇒ Object

A 5' UTR variant where a premature start codon is moved. (http://purl.obolibrary.org/obo/SO_0001990)

# File 'lib/biointerchange/so.rb', line 12143

def self.five_prime_UTR_premature_start_codon_location_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001990')
end

.five_taurinomethyl_two_thiouridine ⇒ Object

5_taurinomethyl_2_thiouridineis a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001379)

# File 'lib/biointerchange/so.rb', line 8539

def self.five_taurinomethyl_two_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001379')
end

.five_taurinomethyluridine ⇒ Object

5_taurinomethyluridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001378)

# File 'lib/biointerchange/so.rb', line 8533

def self.five_taurinomethyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001378')
end

.five_two_prime_O_dimethylcytidine ⇒ Object

5,2'-O-dimethylcytidine is a modified cytidine. (http://purl.obolibrary.org/obo/SO_0001287)

# File 'lib/biointerchange/so.rb', line 7987

def self.five_two_prime_O_dimethylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001287')
end

.five_two_prime_O_dimethyluridine ⇒ Object

5_2_prime_O_dimethyluridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001346)

# File 'lib/biointerchange/so.rb', line 8341

def self.five_two_prime_O_dimethyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001346')
end

.fixed_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001768)

# File 'lib/biointerchange/so.rb', line 10819

def self.fixed_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001768')
end

.flanked ⇒ Object

An attribute describing a region that is bounded either side by a particular kind of region. (http://purl.obolibrary.org/obo/SO_0000357)

# File 'lib/biointerchange/so.rb', line 2463

def self.flanked
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000357')
end

.flanking_region ⇒ Object

The sequences extending on either side of a specific region. (http://purl.obolibrary.org/obo/SO_0000239)

# File 'lib/biointerchange/so.rb', line 1755

def self.flanking_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000239')
end

.flanking_three_prime_quadruplet_recoding_signal ⇒ Object

Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons. (http://purl.obolibrary.org/obo/SO_1001281)

# File 'lib/biointerchange/so.rb', line 13619

def self.flanking_three_prime_quadruplet_recoding_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001281')
end

.FLEX_element ⇒ Object

A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain. (http://purl.obolibrary.org/obo/SO_0001846)

# File 'lib/biointerchange/so.rb', line 11281

def self.FLEX_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001846')
end

.floxed ⇒ Object

An attribute describing sequence that is flanked by Lox-P sites. (http://purl.obolibrary.org/obo/SO_0000359)

# File 'lib/biointerchange/so.rb', line 2469

def self.floxed
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000359')
end

.floxed_gene ⇒ Object

A transgene that is floxed. (http://purl.obolibrary.org/obo/SO_0000363)

# File 'lib/biointerchange/so.rb', line 2493

def self.floxed_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000363')
end

.foldback_element ⇒ Object

A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats. (http://purl.obolibrary.org/obo/SO_0000238)

# File 'lib/biointerchange/so.rb', line 1749

def self.foldback_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000238')
end

.foreign ⇒ Object

An attribute to describe a region from another species. (http://purl.obolibrary.org/obo/SO_0000784)

# File 'lib/biointerchange/so.rb', line 5021

def self.foreign
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000784')
end

.foreign_gene ⇒ Object

A gene that is foreign. (http://purl.obolibrary.org/obo/SO_0000285)

# File 'lib/biointerchange/so.rb', line 2031

def self.foreign_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000285')
end

.foreign_transposable_element ⇒ Object

A transposable element that is foreign. (http://purl.obolibrary.org/obo/SO_0000720)

# File 'lib/biointerchange/so.rb', line 4643

def self.foreign_transposable_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000720')
end

.forkhead_motif ⇒ Object

A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain. (http://purl.obolibrary.org/obo/SO_0001847)

# File 'lib/biointerchange/so.rb', line 11287

def self.forkhead_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001847')
end

.forward ⇒ Object

Forward is an attribute of the feature, where the feature is in the 5' to 3' direction. (http://purl.obolibrary.org/obo/SO_0001030)

# File 'lib/biointerchange/so.rb', line 6455

def self.forward
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001030')
end

.forward_primer ⇒ Object

A single stranded oligo used for polymerase chain reaction. (http://purl.obolibrary.org/obo/SO_0000121)

# File 'lib/biointerchange/so.rb', line 1043

def self.forward_primer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000121')
end

.fosmid ⇒ Object

A cloning vector that utilizes the E. coli F factor. (http://purl.obolibrary.org/obo/SO_0000158)

# File 'lib/biointerchange/so.rb', line 1265

def self.fosmid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000158')
end

.fosmid_clone ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000763)

# File 'lib/biointerchange/so.rb', line 4901

def self.fosmid_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000763')
end

.four_bp_start_codon ⇒ Object

A non-canonical start codon with 4 base pairs. (http://purl.obolibrary.org/obo/SO_1001269)

# File 'lib/biointerchange/so.rb', line 13559

def self.four_bp_start_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001269')
end

.four_cutter_restriction_site ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000244)

# File 'lib/biointerchange/so.rb', line 1785

def self.four_cutter_restriction_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000244')
end

.four_demethylwyosine ⇒ Object

4_demethylwyosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001341)

# File 'lib/biointerchange/so.rb', line 8311

def self.four_demethylwyosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001341')
end

.four_thiouridine ⇒ Object

4_thiouridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001350)

# File 'lib/biointerchange/so.rb', line 8365

def self.four_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001350')
end

.fragment_assembly ⇒ Object

A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths. (http://purl.obolibrary.org/obo/SO_0001249)

# File 'lib/biointerchange/so.rb', line 7759

def self.fragment_assembly
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001249')
end

.fragmentary ⇒ Object

An attribute to describe a feature that is incomplete. (http://purl.obolibrary.org/obo/SO_0000731)

# File 'lib/biointerchange/so.rb', line 4709

def self.fragmentary
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000731')
end

.frame_restoring_sequence_variant ⇒ Object

A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame. (http://purl.obolibrary.org/obo/SO_1000110)

# File 'lib/biointerchange/so.rb', line 13055

def self.frame_restoring_sequence_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000110')
end

.frame_restoring_variant ⇒ Object

A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame. (http://purl.obolibrary.org/obo/SO_0001591)

# File 'lib/biointerchange/so.rb', line 9787

def self.frame_restoring_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001591')
end

.frameshift ⇒ Object

An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3. (http://purl.obolibrary.org/obo/SO_0000865)

# File 'lib/biointerchange/so.rb', line 5471

def self.frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000865')
end

.frameshift_elongation ⇒ Object

A frameshift variant that causes the translational reading frame to be extended relative to the reference feature. (http://purl.obolibrary.org/obo/SO_0001909)

# File 'lib/biointerchange/so.rb', line 11659

def self.frameshift_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001909')
end

.frameshift_sequence_variation ⇒ Object

A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. (http://purl.obolibrary.org/obo/SO_1000065)

# File 'lib/biointerchange/so.rb', line 12803

def self.frameshift_sequence_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000065')
end

.frameshift_truncation ⇒ Object

A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature. (http://purl.obolibrary.org/obo/SO_0001910)

# File 'lib/biointerchange/so.rb', line 11665

def self.frameshift_truncation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001910')
end

.frameshift_variant ⇒ Object

A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. (http://purl.obolibrary.org/obo/SO_0001589)

# File 'lib/biointerchange/so.rb', line 9775

def self.frameshift_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001589')
end

.free ⇒ Object

The quality of a duplication where the new region exists independently of the original. (http://purl.obolibrary.org/obo/SO_0001516)

# File 'lib/biointerchange/so.rb', line 9355

def self.free
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001516')
end

.free_chromosome_arm ⇒ Object

A chromosome structure variation whereby an arm exists as an individual chromosome element. (http://purl.obolibrary.org/obo/SO_0000065)

# File 'lib/biointerchange/so.rb', line 707

def self.free_chromosome_arm
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000065')
end

.free_duplication ⇒ Object

A chromosome structure variation whereby the duplicated sequences are carried as a free centric element. (http://purl.obolibrary.org/obo/SO_1000144)

# File 'lib/biointerchange/so.rb', line 13199

def self.free_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000144')
end

.free_ring_duplication ⇒ Object

A ring chromosome which is a copy of another chromosome. (http://purl.obolibrary.org/obo/SO_1000145)

# File 'lib/biointerchange/so.rb', line 13205

def self.free_ring_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000145')
end

.FRT_flanked ⇒ Object

An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT. (http://purl.obolibrary.org/obo/SO_0000361)

# File 'lib/biointerchange/so.rb', line 2481

def self.FRT_flanked
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000361')
end

.FRT_site ⇒ Object

An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid. (http://purl.obolibrary.org/obo/SO_0000350)

# File 'lib/biointerchange/so.rb', line 2421

def self.FRT_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000350')
end

.functional_candidate_gene ⇒ Object

A candidate gene whose function has something in common biologically with the trait under investigation. (http://purl.obolibrary.org/obo/SO_0001869)

# File 'lib/biointerchange/so.rb', line 11419

def self.functional_candidate_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001869')
end

.functional_variant ⇒ Object

A sequence variant in which the function of a gene product is altered with respect to a reference. (http://purl.obolibrary.org/obo/SO_0001536)

# File 'lib/biointerchange/so.rb', line 9475

def self.functional_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001536')
end

.fusion ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000806)

# File 'lib/biointerchange/so.rb', line 5129

def self.fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000806')
end

.fusion_gene ⇒ Object

A gene that is a fusion. (http://purl.obolibrary.org/obo/SO_0000287)

# File 'lib/biointerchange/so.rb', line 2043

def self.fusion_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000287')
end

.G_box ⇒ Object

A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a. (http://purl.obolibrary.org/obo/SO_0001980)

# File 'lib/biointerchange/so.rb', line 12083

def self.G_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001980')
end

.G_quartet ⇒ Object

G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet. (http://purl.obolibrary.org/obo/SO_0000003)

# File 'lib/biointerchange/so.rb', line 333

def self.G_quartet
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000003')
end

.G_to_A_transition ⇒ Object

A transition of a guanine to an adenine. (http://purl.obolibrary.org/obo/SO_1000016)

# File 'lib/biointerchange/so.rb', line 12539

def self.G_to_A_transition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000016')
end

.G_to_C_transversion ⇒ Object

A transversion from guanine to cytidine. (http://purl.obolibrary.org/obo/SO_1000026)

# File 'lib/biointerchange/so.rb', line 12599

def self.G_to_C_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000026')
end

.G_to_T_transversion ⇒ Object

A transversion from guanine to thymine. (http://purl.obolibrary.org/obo/SO_1000027)

# File 'lib/biointerchange/so.rb', line 12605

def self.G_to_T_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000027')
end

.GAGA_motif ⇒ Object

A non directional promoter motif with consensus sequence GAGAGCG. (http://purl.obolibrary.org/obo/SO_0001166)

# File 'lib/biointerchange/so.rb', line 7267

def self.GAGA_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001166')
end

.gained ⇒ Object

X gained Y if X is a variant_of X' and Y part of X but not X'. (http://purl.obolibrary.org/obo/so_2_5_2.obo#gained)

# File 'lib/biointerchange/so.rb', line 101

def self.gained
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#gained')
end

.galactosyl_queuosine ⇒ Object

Galactosyl_queuosine is a modified 7-deazoguanosine. (http://purl.obolibrary.org/obo/SO_0001319)

# File 'lib/biointerchange/so.rb', line 8179

def self.galactosyl_queuosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001319')
end

.gamma_turn ⇒ Object

Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees. (http://purl.obolibrary.org/obo/SO_0001138)

# File 'lib/biointerchange/so.rb', line 7099

def self.gamma_turn
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001138')
end

.gamma_turn_classic ⇒ Object

Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0. (http://purl.obolibrary.org/obo/SO_0001139)

# File 'lib/biointerchange/so.rb', line 7105

def self.gamma_turn_classic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001139')
end

.gamma_turn_inverse ⇒ Object

Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0. (http://purl.obolibrary.org/obo/SO_0001140)

# File 'lib/biointerchange/so.rb', line 7111

def self.gamma_turn_inverse
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001140')
end

.gap ⇒ Object

A gap in the sequence of known length. The unknown bases are filled in with N's. (http://purl.obolibrary.org/obo/SO_0000730)

# File 'lib/biointerchange/so.rb', line 4703

def self.gap
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000730')
end

.GATA_box ⇒ Object

A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G). (http://purl.obolibrary.org/obo/SO_0001840)

# File 'lib/biointerchange/so.rb', line 11245

def self.GATA_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001840')
end

.GC_rich_promoter_region ⇒ Object

A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG. (http://purl.obolibrary.org/obo/SO_0000173)

# File 'lib/biointerchange/so.rb', line 1355

def self.GC_rich_promoter_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000173')
end

.GcvB_RNA ⇒ Object

A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli. (http://purl.obolibrary.org/obo/SO_0000379)

# File 'lib/biointerchange/so.rb', line 2589

def self.GcvB_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000379')
end

.gene ⇒ Object

A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. (http://purl.obolibrary.org/obo/SO_0000704)

# File 'lib/biointerchange/so.rb', line 4547

def self.gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000704')
end

.gene_array ⇒ Object

An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so. (http://purl.obolibrary.org/obo/SO_0005851)

# File 'lib/biointerchange/so.rb', line 12305

def self.gene_array
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005851')
end

.gene_array_member ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000081)

# File 'lib/biointerchange/so.rb', line 803

def self.gene_array_member
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000081')
end

.gene_attribute ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000401)

# File 'lib/biointerchange/so.rb', line 2721

def self.gene_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000401')
end

.gene_by_genome_location ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000085)

# File 'lib/biointerchange/so.rb', line 827

def self.gene_by_genome_location
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000085')
end

.gene_by_organelle_of_genome ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000086)

# File 'lib/biointerchange/so.rb', line 833

def self.gene_by_organelle_of_genome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000086')
end

.gene_by_polyadenylation_attribute ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000066)

# File 'lib/biointerchange/so.rb', line 713

def self.gene_by_polyadenylation_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000066')
end

.gene_by_transcript_attribute ⇒ Object

This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004. (http://purl.obolibrary.org/obo/SO_0000064)

# File 'lib/biointerchange/so.rb', line 701

def self.gene_by_transcript_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000064')
end

.gene_cassette ⇒ Object

A gene that can be substituted for a related gene at a different site in the genome. (http://purl.obolibrary.org/obo/SO_0005853)

# File 'lib/biointerchange/so.rb', line 12317

def self.gene_cassette
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005853')
end

.gene_cassette_array ⇒ Object

An array of non-functional genes whose members, when captured by recombination form functional genes. (http://purl.obolibrary.org/obo/SO_0005854)

# File 'lib/biointerchange/so.rb', line 12323

def self.gene_cassette_array
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005854')
end

.gene_cassette_member ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0005848)

# File 'lib/biointerchange/so.rb', line 12287

def self.gene_cassette_member
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005848')
end

.gene_class ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000009)

# File 'lib/biointerchange/so.rb', line 369

def self.gene_class
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000009')
end

.gene_component_region ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000842)

# File 'lib/biointerchange/so.rb', line 5333

def self.gene_component_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000842')
end

.gene_fragment ⇒ Object

This term is mapped to MGED. Do not obsolete without consulting MGED ontology. (http://purl.obolibrary.org/obo/SO_0000997)

# File 'lib/biointerchange/so.rb', line 6257

def self.gene_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000997')
end

.gene_fusion ⇒ Object

A sequence variant whereby a two genes have become joined. (http://purl.obolibrary.org/obo/SO_0001565)

# File 'lib/biointerchange/so.rb', line 9649

def self.gene_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001565')
end

.gene_group ⇒ Object

A collection of related genes. (http://purl.obolibrary.org/obo/SO_0005855)

# File 'lib/biointerchange/so.rb', line 12329

def self.gene_group
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005855')
end

.gene_group_regulatory_region ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000752)

# File 'lib/biointerchange/so.rb', line 4835

def self.gene_group_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000752')
end

.gene_member_region ⇒ Object

A region of a gene. (http://purl.obolibrary.org/obo/SO_0000831)

# File 'lib/biointerchange/so.rb', line 5267

def self.gene_member_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000831')
end

.gene_not_polyadenylated ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000438)

# File 'lib/biointerchange/so.rb', line 2947

def self.gene_not_polyadenylated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000438')
end

.gene_part ⇒ Object

A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene. (http://purl.obolibrary.org/obo/SO_0000050)

# File 'lib/biointerchange/so.rb', line 609

def self.gene_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000050')
end

.gene_rearranged_at_DNA_level ⇒ Object

An epigenetically modified gene, rearranged at the DNA level. (http://purl.obolibrary.org/obo/SO_0000138)

# File 'lib/biointerchange/so.rb', line 1145

def self.gene_rearranged_at_DNA_level
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000138')
end

.gene_segment ⇒ Object

A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination. (http://purl.obolibrary.org/obo/SO_3000000)

# File 'lib/biointerchange/so.rb', line 13673

def self.gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_3000000')
end

.gene_sensu_your_favorite_organism ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000008)

# File 'lib/biointerchange/so.rb', line 363

def self.gene_sensu_your_favorite_organism
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000008')
end

.gene_silenced_by_DNA_methylation ⇒ Object

A gene that is silenced by DNA methylation. (http://purl.obolibrary.org/obo/SO_0000129)

# File 'lib/biointerchange/so.rb', line 1091

def self.gene_silenced_by_DNA_methylation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000129')
end

.gene_silenced_by_DNA_modification ⇒ Object

A gene that is silenced by DNA modification. (http://purl.obolibrary.org/obo/SO_0000128)

# File 'lib/biointerchange/so.rb', line 1085

def self.gene_silenced_by_DNA_modification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000128')
end

.gene_silenced_by_histone_deacetylation ⇒ Object

A gene that is silenced by histone deacetylation. (http://purl.obolibrary.org/obo/SO_0001227)

# File 'lib/biointerchange/so.rb', line 7633

def self.gene_silenced_by_histone_deacetylation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001227')
end

.gene_silenced_by_histone_methylation ⇒ Object

A gene that is silenced by histone methylation. (http://purl.obolibrary.org/obo/SO_0001226)

# File 'lib/biointerchange/so.rb', line 7627

def self.gene_silenced_by_histone_methylation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001226')
end

.gene_silenced_by_histone_modification ⇒ Object

A gene that is silenced by histone modification. (http://purl.obolibrary.org/obo/SO_0001225)

# File 'lib/biointerchange/so.rb', line 7621

def self.gene_silenced_by_histone_modification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001225')
end

.gene_silenced_by_RNA_interference ⇒ Object

A gene that is silenced by RNA interference. (http://purl.obolibrary.org/obo/SO_0001224)

# File 'lib/biointerchange/so.rb', line 7615

def self.gene_silenced_by_RNA_interference
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001224')
end

.gene_subarray ⇒ Object

A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function. (http://purl.obolibrary.org/obo/SO_0005852)

# File 'lib/biointerchange/so.rb', line 12311

def self.gene_subarray
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005852')
end

.gene_subarray_member ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0005849)

# File 'lib/biointerchange/so.rb', line 12293

def self.gene_subarray_member
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005849')
end

.gene_to_gene_feature ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000067)

# File 'lib/biointerchange/so.rb', line 719

def self.gene_to_gene_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000067')
end

.gene_trap_construct ⇒ Object

A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker. (http://purl.obolibrary.org/obo/SO_0001477)

# File 'lib/biointerchange/so.rb', line 9121

def self.gene_trap_construct
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001477')
end

.gene_variant ⇒ Object

A sequence variant where the structure of the gene is changed. (http://purl.obolibrary.org/obo/SO_0001564)

# File 'lib/biointerchange/so.rb', line 9643

def self.gene_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001564')
end

.gene_with_dicistronic_mRNA ⇒ Object

A gene that encodes a polycistronic mRNA. (http://purl.obolibrary.org/obo/SO_0000722)

# File 'lib/biointerchange/so.rb', line 4655

def self.gene_with_dicistronic_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000722')
end

.gene_with_dicistronic_primary_transcript ⇒ Object

A gene that encodes a dicistronic primary transcript. (http://purl.obolibrary.org/obo/SO_0000721)

# File 'lib/biointerchange/so.rb', line 4649

def self.gene_with_dicistronic_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000721')
end

.gene_with_dicistronic_transcript ⇒ Object

A gene that encodes a dicistronic transcript. (http://purl.obolibrary.org/obo/SO_0000692)

# File 'lib/biointerchange/so.rb', line 4475

def self.gene_with_dicistronic_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000692')
end

.gene_with_edited_transcript ⇒ Object

A gene that encodes a transcript that is edited. (http://purl.obolibrary.org/obo/SO_0000548)

# File 'lib/biointerchange/so.rb', line 3607

def self.gene_with_edited_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000548')
end

.gene_with_mRNA_recoded_by_translational_bypass ⇒ Object

A gene with mRNA recoded by translational bypass. (http://purl.obolibrary.org/obo/SO_0000711)

# File 'lib/biointerchange/so.rb', line 4589

def self.gene_with_mRNA_recoded_by_translational_bypass
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000711')
end

.gene_with_mRNA_with_frameshift ⇒ Object

A gene that encodes an mRNA with a frameshift. (http://purl.obolibrary.org/obo/SO_0000455)

# File 'lib/biointerchange/so.rb', line 3049

def self.gene_with_mRNA_with_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000455')
end

.gene_with_non_canonical_start_codon ⇒ Object

A gene with a start codon other than AUG. (http://purl.obolibrary.org/obo/SO_0001739)

# File 'lib/biointerchange/so.rb', line 10645

def self.gene_with_non_canonical_start_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001739')
end

.gene_with_polyadenylated_mRNA ⇒ Object

A gene that encodes a polyadenylated mRNA. (http://purl.obolibrary.org/obo/SO_0000451)

# File 'lib/biointerchange/so.rb', line 3025

def self.gene_with_polyadenylated_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000451')
end

.gene_with_polycistronic_transcript ⇒ Object

A gene that encodes a polycistronic transcript. (http://purl.obolibrary.org/obo/SO_0000690)

# File 'lib/biointerchange/so.rb', line 4463

def self.gene_with_polycistronic_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000690')
end

.gene_with_recoded_mRNA ⇒ Object

A gene that encodes an mRNA that is recoded. (http://purl.obolibrary.org/obo/SO_0000693)

# File 'lib/biointerchange/so.rb', line 4481

def self.gene_with_recoded_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000693')
end

.gene_with_start_codon_CUG ⇒ Object

A gene with a translational start codon of CUG. (http://purl.obolibrary.org/obo/SO_0001740)

# File 'lib/biointerchange/so.rb', line 10651

def self.gene_with_start_codon_CUG
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001740')
end

.gene_with_stop_codon_read_through ⇒ Object

A gene that encodes a transcript with stop codon readthrough. (http://purl.obolibrary.org/obo/SO_0000697)

# File 'lib/biointerchange/so.rb', line 4505

def self.gene_with_stop_codon_read_through
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000697')
end

.gene_with_stop_codon_redefined_as_pyrrolysine ⇒ Object

A gene encoding an mRNA that has the stop codon redefined as pyrrolysine. (http://purl.obolibrary.org/obo/SO_0000698)

# File 'lib/biointerchange/so.rb', line 4511

def self.gene_with_stop_codon_redefined_as_pyrrolysine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000698')
end

.gene_with_stop_codon_redefined_as_selenocysteine ⇒ Object

A gene encoding an mRNA that has the stop codon redefined as selenocysteine. (http://purl.obolibrary.org/obo/SO_0000710)

# File 'lib/biointerchange/so.rb', line 4583

def self.gene_with_stop_codon_redefined_as_selenocysteine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000710')
end

.gene_with_trans_spliced_transcript ⇒ Object

A gene with a transcript that is trans-spliced. (http://purl.obolibrary.org/obo/SO_0000459)

# File 'lib/biointerchange/so.rb', line 3073

def self.gene_with_trans_spliced_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000459')
end

.gene_with_transcript_with_translational_frameshift ⇒ Object

A gene encoding a transcript that has a translational frameshift. (http://purl.obolibrary.org/obo/SO_0000712)

# File 'lib/biointerchange/so.rb', line 4595

def self.gene_with_transcript_with_translational_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000712')
end

.genetic_marker ⇒ Object

A measurable sequence feature that varies within a population. (http://purl.obolibrary.org/obo/SO_0001645)

# File 'lib/biointerchange/so.rb', line 10105

def self.genetic_marker
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001645')
end

.genome ⇒ Object

A genome is the sum of genetic material within a cell or virion. (http://purl.obolibrary.org/obo/SO_0001026)

# File 'lib/biointerchange/so.rb', line 6431

def self.genome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001026')
end

.genome_of ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#genome_of)

# File 'lib/biointerchange/so.rb', line 107

def self.genome_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#genome_of')
end

.genomic_clone ⇒ Object

A clone of a DNA region of a genome. (http://purl.obolibrary.org/obo/SO_0000040)

# File 'lib/biointerchange/so.rb', line 549

def self.genomic_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000040')
end

.genomic_DNA ⇒ Object

This term is mapped to MGED. Do not obsolete without consulting MGED ontology. (http://purl.obolibrary.org/obo/SO_0000991)

# File 'lib/biointerchange/so.rb', line 6221

def self.genomic_DNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000991')
end

.genomic_DNA_read ⇒ Object

A sequencer read of a genomic DNA substrate. (http://purl.obolibrary.org/obo/SO_0001828)

# File 'lib/biointerchange/so.rb', line 11173

def self.genomic_DNA_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001828')
end

.genomic_island ⇒ Object

A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility. (http://purl.obolibrary.org/obo/SO_0000772)

# File 'lib/biointerchange/so.rb', line 4949

def self.genomic_island
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000772')
end

.genomically_contaminated_cDNA_clone ⇒ Object

A cDNA clone invalidated by genomic contamination. (http://purl.obolibrary.org/obo/SO_0000811)

# File 'lib/biointerchange/so.rb', line 5159

def self.genomically_contaminated_cDNA_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000811')
end

.genomically_imprinted ⇒ Object

Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin. (http://purl.obolibrary.org/obo/SO_0000134)

# File 'lib/biointerchange/so.rb', line 1121

def self.genomically_imprinted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000134')
end

.genotype ⇒ Object

A genotype is a variant genome, complete or incomplete. (http://purl.obolibrary.org/obo/SO_0001027)

# File 'lib/biointerchange/so.rb', line 6437

def self.genotype
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001027')
end

.germline_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001778)

# File 'lib/biointerchange/so.rb', line 10879

def self.germline_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001778')
end

.glutamic_acid ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001454)

# File 'lib/biointerchange/so.rb', line 8983

def self.glutamic_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001454')
end

.glutamic_acid_tRNA_primary_transcript ⇒ Object

A primary transcript encoding glutaminyl tRNA (SO:0000260). (http://purl.obolibrary.org/obo/SO_0000216)

# File 'lib/biointerchange/so.rb', line 1617

def self.glutamic_acid_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000216')
end

.glutamine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001448)

# File 'lib/biointerchange/so.rb', line 8947

def self.glutamine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001448')
end

.glutamine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding glutamyl tRNA (SO:0000260). (http://purl.obolibrary.org/obo/SO_0000217)

# File 'lib/biointerchange/so.rb', line 1623

def self.glutamine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000217')
end

.glutaminyl_tRNA ⇒ Object

A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region. (http://purl.obolibrary.org/obo/SO_0000259)

# File 'lib/biointerchange/so.rb', line 1875

def self.glutaminyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000259')
end

.glutamyl_tRNA ⇒ Object

A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region. (http://purl.obolibrary.org/obo/SO_0000260)

# File 'lib/biointerchange/so.rb', line 1881

def self.glutamyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000260')
end

.glycine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001443)

# File 'lib/biointerchange/so.rb', line 8917

def self.glycine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001443')
end

.glycine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding glycyl tRNA (SO:0000263). (http://purl.obolibrary.org/obo/SO_0000218)

# File 'lib/biointerchange/so.rb', line 1629

def self.glycine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000218')
end

.glycyl_tRNA ⇒ Object

A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region. (http://purl.obolibrary.org/obo/SO_0000261)

# File 'lib/biointerchange/so.rb', line 1887

def self.glycyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000261')
end

.GNA ⇒ Object

An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA. (http://purl.obolibrary.org/obo/SO_0001192)

# File 'lib/biointerchange/so.rb', line 7423

def self.GNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001192')
end

.GNA_oligo ⇒ Object

An oligo composed of GNA residues. (http://purl.obolibrary.org/obo/SO_0001193)

# File 'lib/biointerchange/so.rb', line 7429

def self.GNA_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001193')
end

.golden_path ⇒ Object

A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence. (http://purl.obolibrary.org/obo/SO_0000688)

# File 'lib/biointerchange/so.rb', line 4451

def self.golden_path
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000688')
end

.golden_path_fragment ⇒ Object

One of the pieces of sequence that make up a golden path. (http://purl.obolibrary.org/obo/SO_0000468)

# File 'lib/biointerchange/so.rb', line 3127

def self.golden_path_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000468')
end

.gRNA_encoding ⇒ Object

A non-protein_coding gene that encodes a guide_RNA. (http://purl.obolibrary.org/obo/SO_0000979)

# File 'lib/biointerchange/so.rb', line 6149

def self.gRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000979')
end

.gRNA_gene ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001264)

# File 'lib/biointerchange/so.rb', line 7849

def self.gRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001264')
end

.group_1_intron_homing_endonuclease_target_region ⇒ Object

A region of intronic nucleotide sequence targeted by a nuclease enzyme. (http://purl.obolibrary.org/obo/SO_0000354)

# File 'lib/biointerchange/so.rb', line 2445

def self.group_1_intron_homing_endonuclease_target_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000354')
end

.group_I_intron ⇒ Object

Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions. (http://purl.obolibrary.org/obo/SO_0000587)

# File 'lib/biointerchange/so.rb', line 3845

def self.group_I_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000587')
end

.group_II_intron ⇒ Object

Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny. (http://purl.obolibrary.org/obo/SO_0000603)

# File 'lib/biointerchange/so.rb', line 3941

def self.group_II_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000603')
end

.group_IIA_intron ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000381)

# File 'lib/biointerchange/so.rb', line 2601

def self.group_IIA_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000381')
end

.group_IIB_intron ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000382)

# File 'lib/biointerchange/so.rb', line 2607

def self.group_IIB_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000382')
end

.group_III_intron ⇒ Object

Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile. (http://purl.obolibrary.org/obo/SO_0001213)

# File 'lib/biointerchange/so.rb', line 7549

def self.group_III_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001213')
end

.GT_dinucleotide_repeat ⇒ Object

A dinucleotide repeat region composed of GT repeating elements. (http://purl.obolibrary.org/obo/SO_0001862)

# File 'lib/biointerchange/so.rb', line 11377

def self.GT_dinucleotide_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001862')
end

.GTT_trinucleotide_repeat ⇒ Object

A trinucleotide repeat region composed of GTT repeating elements. (http://purl.obolibrary.org/obo/SO_0001863)

# File 'lib/biointerchange/so.rb', line 11383

def self.GTT_trinucleotide_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001863')
end

.guide_RNA ⇒ Object

A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA. (http://purl.obolibrary.org/obo/SO_0000602)

# File 'lib/biointerchange/so.rb', line 3935

def self.guide_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000602')
end

.guide_RNA_region ⇒ Object

A region of guide RNA. (http://purl.obolibrary.org/obo/SO_0000930)

# File 'lib/biointerchange/so.rb', line 5861

def self.guide_RNA_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000930')
end

.guided_by ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#guided_by)

# File 'lib/biointerchange/so.rb', line 113

def self.guided_by
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#guided_by')
end

.guides ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#guides)

# File 'lib/biointerchange/so.rb', line 119

def self.guides
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#guides')
end

.H2AK5_acetylation_site ⇒ Object

A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated. (http://purl.obolibrary.org/obo/SO_0001938)

# File 'lib/biointerchange/so.rb', line 11833

def self.H2AK5_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001938')
end

.H2AK9_acetylation_site ⇒ Object

A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated. (http://purl.obolibrary.org/obo/SO_0001944)

# File 'lib/biointerchange/so.rb', line 11869

def self.H2AK9_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001944')
end

.H2B_ubiquitination_site ⇒ Object

A histone modification site on H2B where ubiquitin may be added. (http://purl.obolibrary.org/obo/SO_0001717)

# File 'lib/biointerchange/so.rb', line 10513

def self.H2B_ubiquitination_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001717')
end

.H2BK120_acetylation_site ⇒ Object

A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated. (http://purl.obolibrary.org/obo/SO_0001940)

# File 'lib/biointerchange/so.rb', line 11845

def self.H2BK120_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001940')
end

.H2BK12_acetylation_site ⇒ Object

A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated. (http://purl.obolibrary.org/obo/SO_0001937)

# File 'lib/biointerchange/so.rb', line 11827

def self.H2BK12_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001937')
end

.H2BK15_acetylation_site ⇒ Object

A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated. (http://purl.obolibrary.org/obo/SO_0001946)

# File 'lib/biointerchange/so.rb', line 11881

def self.H2BK15_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001946')
end

.H2BK20_acetylation_site ⇒ Object

A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated. (http://purl.obolibrary.org/obo/SO_0001942)

# File 'lib/biointerchange/so.rb', line 11857

def self.H2BK20_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001942')
end

.H2BK5_monomethylation_site ⇒ Object

A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated. (http://purl.obolibrary.org/obo/SO_0001714)

# File 'lib/biointerchange/so.rb', line 10495

def self.H2BK5_monomethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001714')
end

.H3K14_acetylation_site ⇒ Object

A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated. (http://purl.obolibrary.org/obo/SO_0001704)

# File 'lib/biointerchange/so.rb', line 10435

def self.H3K14_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001704')
end

.H3K18_acetylation_site ⇒ Object

A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated. (http://purl.obolibrary.org/obo/SO_0001718)

# File 'lib/biointerchange/so.rb', line 10519

def self.H3K18_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001718')
end

.H3K20_trimethylation_site ⇒ Object

A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated. (http://purl.obolibrary.org/obo/SO_0001935)

# File 'lib/biointerchange/so.rb', line 11815

def self.H3K20_trimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001935')
end

.H3K23_acylation_site ⇒ Object

A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated. (http://purl.obolibrary.org/obo/SO_0001719)

# File 'lib/biointerchange/so.rb', line 10525

def self.H3K23_acylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001719')
end

.H3K23_dimethylation_site ⇒ Object

A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated. (http://purl.obolibrary.org/obo/SO_0001951)

# File 'lib/biointerchange/so.rb', line 11911

def self.H3K23_dimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001951')
end

.H3K27_acylation_site ⇒ Object

A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated. (http://purl.obolibrary.org/obo/SO_0001721)

# File 'lib/biointerchange/so.rb', line 10537

def self.H3K27_acylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001721')
end

.H3K27_dimethylation_site ⇒ Object

A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated. (http://purl.obolibrary.org/obo/SO_0001726)

# File 'lib/biointerchange/so.rb', line 10567

def self.H3K27_dimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001726')
end

.H3K27_methylation_site ⇒ Object

A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated. (http://purl.obolibrary.org/obo/SO_0001732)

# File 'lib/biointerchange/so.rb', line 10603

def self.H3K27_methylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001732')
end

.H3K27_monomethylation_site ⇒ Object

A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated. (http://purl.obolibrary.org/obo/SO_0001708)

# File 'lib/biointerchange/so.rb', line 10459

def self.H3K27_monomethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001708')
end

.H3K27_trimethylation_site ⇒ Object

A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated. (http://purl.obolibrary.org/obo/SO_0001709)

# File 'lib/biointerchange/so.rb', line 10465

def self.H3K27_trimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001709')
end

.H3K36_acetylation_site ⇒ Object

A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated. (http://purl.obolibrary.org/obo/SO_0001936)

# File 'lib/biointerchange/so.rb', line 11821

def self.H3K36_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001936')
end

.H3K36_dimethylation_site ⇒ Object

A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated. (http://purl.obolibrary.org/obo/SO_0001723)

# File 'lib/biointerchange/so.rb', line 10549

def self.H3K36_dimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001723')
end

.H3K36_methylation_site ⇒ Object

A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated. (http://purl.obolibrary.org/obo/SO_0001733)

# File 'lib/biointerchange/so.rb', line 10609

def self.H3K36_methylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001733')
end

.H3K36_monomethylation_site ⇒ Object

A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated. (http://purl.obolibrary.org/obo/SO_0001722)

# File 'lib/biointerchange/so.rb', line 10543

def self.H3K36_monomethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001722')
end

.H3K36_trimethylation_site ⇒ Object

A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated. (http://purl.obolibrary.org/obo/SO_0001724)

# File 'lib/biointerchange/so.rb', line 10555

def self.H3K36_trimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001724')
end

.H3K4_dimethylation_site ⇒ Object

A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated. (http://purl.obolibrary.org/obo/SO_0001725)

# File 'lib/biointerchange/so.rb', line 10561

def self.H3K4_dimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001725')
end

.H3K4_methylation_site ⇒ Object

A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated. (http://purl.obolibrary.org/obo/SO_0001734)

# File 'lib/biointerchange/so.rb', line 10615

def self.H3K4_methylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001734')
end

.H3K4_monomethylation_site ⇒ Object

A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated. (http://purl.obolibrary.org/obo/SO_0001705)

# File 'lib/biointerchange/so.rb', line 10441

def self.H3K4_monomethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001705')
end

.H3K4_trimethylation ⇒ Object

A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated. (http://purl.obolibrary.org/obo/SO_0001706)

# File 'lib/biointerchange/so.rb', line 10447

def self.H3K4_trimethylation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001706')
end

.H3K4ac_acetylation_site ⇒ Object

A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated. (http://purl.obolibrary.org/obo/SO_0001943)

# File 'lib/biointerchange/so.rb', line 11863

def self.H3K4ac_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001943')
end

.H3K56_acetylation_site ⇒ Object

A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated. (http://purl.obolibrary.org/obo/SO_0001945)

# File 'lib/biointerchange/so.rb', line 11875

def self.H3K56_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001945')
end

.H3K79_dimethylation_site ⇒ Object

A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated. (http://purl.obolibrary.org/obo/SO_0001711)

# File 'lib/biointerchange/so.rb', line 10477

def self.H3K79_dimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001711')
end

.H3K79_methylation_site ⇒ Object

A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated. (http://purl.obolibrary.org/obo/SO_0001735)

# File 'lib/biointerchange/so.rb', line 10621

def self.H3K79_methylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001735')
end

.H3K79_monomethylation_site ⇒ Object

A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated. (http://purl.obolibrary.org/obo/SO_0001710)

# File 'lib/biointerchange/so.rb', line 10471

def self.H3K79_monomethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001710')
end

.H3K79_trimethylation_site ⇒ Object

A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated. (http://purl.obolibrary.org/obo/SO_0001712)

# File 'lib/biointerchange/so.rb', line 10483

def self.H3K79_trimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001712')
end

.H3K9_acetylation_site ⇒ Object

A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated. (http://purl.obolibrary.org/obo/SO_0001703)

# File 'lib/biointerchange/so.rb', line 10429

def self.H3K9_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001703')
end

.H3K9_dimethylation_site ⇒ Object

A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated. (http://purl.obolibrary.org/obo/SO_0001728)

# File 'lib/biointerchange/so.rb', line 10579

def self.H3K9_dimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001728')
end

.H3K9_methylation_site ⇒ Object

A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated. (http://purl.obolibrary.org/obo/SO_0001736)

# File 'lib/biointerchange/so.rb', line 10627

def self.H3K9_methylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001736')
end

.H3K9_monomethylation_site ⇒ Object

A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated. (http://purl.obolibrary.org/obo/SO_0001727)

# File 'lib/biointerchange/so.rb', line 10573

def self.H3K9_monomethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001727')
end

.H3K9_trimethylation_site ⇒ Object

A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated. (http://purl.obolibrary.org/obo/SO_0001707)

# File 'lib/biointerchange/so.rb', line 10453

def self.H3K9_trimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001707')
end

.H3R2_dimethylation_site ⇒ Object

A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated. (http://purl.obolibrary.org/obo/SO_0001948)

# File 'lib/biointerchange/so.rb', line 11893

def self.H3R2_dimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001948')
end

.H3R2_monomethylation_site ⇒ Object

A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated. (http://purl.obolibrary.org/obo/SO_0001947)

# File 'lib/biointerchange/so.rb', line 11887

def self.H3R2_monomethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001947')
end

.H4K12_acetylation_site ⇒ Object

A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated. (http://purl.obolibrary.org/obo/SO_0001939)

# File 'lib/biointerchange/so.rb', line 11839

def self.H4K12_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001939')
end

.H4K16_acylation_site ⇒ Object

A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated. (http://purl.obolibrary.org/obo/SO_0001729)

# File 'lib/biointerchange/so.rb', line 10585

def self.H4K16_acylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001729')
end

.H4K20_monomethylation_site ⇒ Object

A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated. (http://purl.obolibrary.org/obo/SO_0001713)

# File 'lib/biointerchange/so.rb', line 10489

def self.H4K20_monomethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001713')
end

.H4K4_trimethylation_site ⇒ Object

A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated. (http://purl.obolibrary.org/obo/SO_0001950)

# File 'lib/biointerchange/so.rb', line 11905

def self.H4K4_trimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001950')
end

.H4K5_acylation_site ⇒ Object

A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated. (http://purl.obolibrary.org/obo/SO_0001730)

# File 'lib/biointerchange/so.rb', line 10591

def self.H4K5_acylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001730')
end

.H4K8_acylation_site ⇒ Object

A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated. (http://purl.obolibrary.org/obo/SO_0001731)

# File 'lib/biointerchange/so.rb', line 10597

def self.H4K8_acylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001731')
end

.H4K91_acetylation_site ⇒ Object

A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated. (http://purl.obolibrary.org/obo/SO_0001941)

# File 'lib/biointerchange/so.rb', line 11851

def self.H4K91_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001941')
end

.H4K_acylation_region ⇒ Object

A region of the H4 histone whereby multiple lysines are acylated. (http://purl.obolibrary.org/obo/SO_0001738)

# File 'lib/biointerchange/so.rb', line 10639

def self.H4K_acylation_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001738')
end

.H4R3_dimethylation_site ⇒ Object

A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated. (http://purl.obolibrary.org/obo/SO_0001949)

# File 'lib/biointerchange/so.rb', line 11899

def self.H4R3_dimethylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001949')
end

.H_ACA_box_snoRNA ⇒ Object

Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains. (http://purl.obolibrary.org/obo/SO_0000594)

# File 'lib/biointerchange/so.rb', line 3887

def self.H_ACA_box_snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000594')
end

.H_ACA_box_snoRNA_encoding ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000608)

# File 'lib/biointerchange/so.rb', line 3971

def self.H_ACA_box_snoRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000608')
end

.H_ACA_box_snoRNA_primary_transcript ⇒ Object

A primary transcript encoding a small nucleolar RNA of the box H/ACA family. (http://purl.obolibrary.org/obo/SO_0000596)

# File 'lib/biointerchange/so.rb', line 3899

def self.H_ACA_box_snoRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000596')
end

.H_pseudoknot ⇒ Object

A pseudoknot which contains two stems and at least two loops. (http://purl.obolibrary.org/obo/SO_0000592)

# File 'lib/biointerchange/so.rb', line 3875

def self.H_pseudoknot
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000592')
end

.hammerhead_ribozyme ⇒ Object

A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs. (http://purl.obolibrary.org/obo/SO_0000380)

# File 'lib/biointerchange/so.rb', line 2595

def self.hammerhead_ribozyme
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000380')
end

.haplotype ⇒ Object

A haplotype is one of a set of coexisting sequence variants of a haplotype block. (http://purl.obolibrary.org/obo/SO_0001024)

# File 'lib/biointerchange/so.rb', line 6419

def self.haplotype
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001024')
end

.haplotype_block ⇒ Object

A region of the genome which is co-inherited as the result of the lack of historic recombination within it. (http://purl.obolibrary.org/obo/SO_0000355)

# File 'lib/biointerchange/so.rb', line 2451

def self.haplotype_block
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000355')
end

.has_integral_part ⇒ Object

X has_integral_part Y if and only if: X has_part Y and Y part_of X. (http://purl.obolibrary.org/obo/so_2_5_2.obo#has_integral_part)

# File 'lib/biointerchange/so.rb', line 125

def self.has_integral_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#has_integral_part')
end

.has_origin ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#has_origin)

# File 'lib/biointerchange/so.rb', line 131

def self.has_origin
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#has_origin')
end

.has_parent?(uri, parent) ⇒ Boolean

Recursively tries to determine the parent for a given URI.

uri

URI that is tested for whether it has the given parent URI.

parent

Parent URI.

Returns:

• (Boolean)

# File 'lib/biointerchange/so.rb', line 20563

def self.has_parent?(uri, parent)
  if @@parent_properties.has_key?(uri) then
    if @@parent_properties[uri] == parent then
      return true
    end
    return has_parent?(@@parent_properties[uri], parent)
  end
  return false
end

.has_part ⇒ Object

Inverse of part_of. (http://purl.obolibrary.org/obo/so_2_5_2.obo#has_part)

# File 'lib/biointerchange/so.rb', line 137

def self.has_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#has_part')
end

.has_quality ⇒ Object

The relationship between a feature and an attribute. (http://purl.obolibrary.org/obo/so_2_5_2.obo#has_quality)

# File 'lib/biointerchange/so.rb', line 143

def self.has_quality
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#has_quality')
end

.helitron ⇒ Object

A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons. (http://purl.obolibrary.org/obo/SO_0000544)

# File 'lib/biointerchange/so.rb', line 3583

def self.helitron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000544')
end

.helix_turn_helix ⇒ Object

A motif comprising two helices separated by a turn. (http://purl.obolibrary.org/obo/SO_0001081)

# File 'lib/biointerchange/so.rb', line 6757

def self.helix_turn_helix
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001081')
end

.heptamer_of_recombination_feature_of_vertebrate_immune_system_gene ⇒ Object

Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene. (http://purl.obolibrary.org/obo/SO_0000561)

# File 'lib/biointerchange/so.rb', line 3689

def self.heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000561')
end

.heritable_phenotypic_marker ⇒ Object

A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus. (http://purl.obolibrary.org/obo/SO_0001500)

# File 'lib/biointerchange/so.rb', line 9259

def self.heritable_phenotypic_marker
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001500')
end

.hetero_compound_chromosome ⇒ Object

A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them. (http://purl.obolibrary.org/obo/SO_1000140)

# File 'lib/biointerchange/so.rb', line 13175

def self.hetero_compound_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000140')
end

.high_identity_region ⇒ Object

An experimental feature with high sequence identity to another sequence. (http://purl.obolibrary.org/obo/SO_0001502)

# File 'lib/biointerchange/so.rb', line 9271

def self.high_identity_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001502')
end

.high_quality_draft ⇒ Object

The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome. (http://purl.obolibrary.org/obo/SO_0001487)

# File 'lib/biointerchange/so.rb', line 9181

def self.high_quality_draft
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001487')
end

.histidine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001452)

# File 'lib/biointerchange/so.rb', line 8971

def self.histidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001452')
end

.histidine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding histidyl tRNA (SO:0000262). (http://purl.obolibrary.org/obo/SO_0000219)

# File 'lib/biointerchange/so.rb', line 1635

def self.histidine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000219')
end

.histidyl_tRNA ⇒ Object

A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region. (http://purl.obolibrary.org/obo/SO_0000262)

# File 'lib/biointerchange/so.rb', line 1893

def self.histidyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000262')
end

.histone_3_acetylation_site ⇒ Object

A histone 3 modification where the modification is the acylation of the residue. (http://purl.obolibrary.org/obo/SO_0001973)

# File 'lib/biointerchange/so.rb', line 12047

def self.histone_3_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001973')
end

.histone_4_acylation_site ⇒ Object

A histone 4 modification where the modification is the acylation of the residue. (http://purl.obolibrary.org/obo/SO_0001972)

# File 'lib/biointerchange/so.rb', line 12041

def self.histone_4_acylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001972')
end

.histone_acetylation_site ⇒ Object

A histone modification where the modification is the acylation of the residue. (http://purl.obolibrary.org/obo/SO_0001702)

# File 'lib/biointerchange/so.rb', line 10423

def self.histone_acetylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001702')
end

.histone_acylation_region ⇒ Object

A histone modification, whereby the histone protein is acylated at multiple sites in a region. (http://purl.obolibrary.org/obo/SO_0001737)

# File 'lib/biointerchange/so.rb', line 10633

def self.histone_acylation_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001737')
end

.histone_binding_site ⇒ Object

A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone. (http://purl.obolibrary.org/obo/SO_0001383)

# File 'lib/biointerchange/so.rb', line 8563

def self.histone_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001383')
end

.histone_methylation_site ⇒ Object

A histone modification site where the modification is the methylation of the residue. (http://purl.obolibrary.org/obo/SO_0001701)

# File 'lib/biointerchange/so.rb', line 10417

def self.histone_methylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001701')
end

.histone_modification ⇒ Object

Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation. (http://purl.obolibrary.org/obo/SO_0001700)

# File 'lib/biointerchange/so.rb', line 10411

def self.histone_modification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001700')
end

.histone_ubiqitination_site ⇒ Object

A histone modification site where ubiquitin may be added. (http://purl.obolibrary.org/obo/SO_0001716)

# File 'lib/biointerchange/so.rb', line 10507

def self.histone_ubiqitination_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001716')
end

.homing_endonuclease_binding_site ⇒ Object

The binding site (recognition site) of a homing endonuclease. The binding site is typically large. (http://purl.obolibrary.org/obo/SO_0001257)

# File 'lib/biointerchange/so.rb', line 7807

def self.homing_endonuclease_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001257')
end

.homo_compound_chromosome ⇒ Object

A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved. (http://purl.obolibrary.org/obo/SO_1000138)

# File 'lib/biointerchange/so.rb', line 13169

def self.homo_compound_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000138')
end

.homol_D_box ⇒ Object

A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence. (http://purl.obolibrary.org/obo/SO_0001848)

# File 'lib/biointerchange/so.rb', line 11293

def self.homol_D_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001848')
end

.homol_E_box ⇒ Object

A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence. (http://purl.obolibrary.org/obo/SO_0001849)

# File 'lib/biointerchange/so.rb', line 11299

def self.homol_E_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001849')
end

.homologous ⇒ Object

Similarity due to common ancestry. (http://purl.obolibrary.org/obo/SO_0000857)

# File 'lib/biointerchange/so.rb', line 5423

def self.homologous
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000857')
end

.homologous_region ⇒ Object

A region that is homologous to another region. (http://purl.obolibrary.org/obo/SO_0000853)

# File 'lib/biointerchange/so.rb', line 5399

def self.homologous_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000853')
end

.homologous_to ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#homologous_to)

# File 'lib/biointerchange/so.rb', line 149

def self.homologous_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#homologous_to')
end

.Hoogsteen_base_pair ⇒ Object

A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds. (http://purl.obolibrary.org/obo/SO_0000500)

# File 'lib/biointerchange/so.rb', line 3319

def self.Hoogsteen_base_pair
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000500')
end

.HSE ⇒ Object

A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF. (http://purl.obolibrary.org/obo/SO_0001850)

# File 'lib/biointerchange/so.rb', line 11305

def self.HSE
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001850')
end

.hydrophobic_region_of_peptide ⇒ Object

Hydrophobic regions are regions with a low affinity for water. (http://purl.obolibrary.org/obo/SO_0100013)

# File 'lib/biointerchange/so.rb', line 12425

def self.hydrophobic_region_of_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100013')
end

.hydroxywybutosine ⇒ Object

Hydroxywybutosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001334)

# File 'lib/biointerchange/so.rb', line 8269

def self.hydroxywybutosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001334')
end

.hyperploid ⇒ Object

A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present. (http://purl.obolibrary.org/obo/SO_0000055)

# File 'lib/biointerchange/so.rb', line 643

def self.hyperploid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000055')
end

.hypoploid ⇒ Object

A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing. (http://purl.obolibrary.org/obo/SO_0000056)

# File 'lib/biointerchange/so.rb', line 649

def self.hypoploid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000056')
end

.I_box ⇒ Object

A plant regulatory promoter motif, composed of a highly conserved hexamer GATAAG (I-box core). (http://purl.obolibrary.org/obo/SO_0001982)

# File 'lib/biointerchange/so.rb', line 12095

def self.I_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001982')
end

.i_motif ⇒ Object

A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH. (http://purl.obolibrary.org/obo/SO_0001010)

# File 'lib/biointerchange/so.rb', line 6335

def self.i_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001010')
end

.iDNA ⇒ Object

Genomic sequence removed from the genome, as a normal event, by a process of recombination. (http://purl.obolibrary.org/obo/SO_0000723)

# File 'lib/biointerchange/so.rb', line 4661

def self.iDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000723')
end

.immature_peptide_region ⇒ Object

An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs. (http://purl.obolibrary.org/obo/SO_0001063)

# File 'lib/biointerchange/so.rb', line 6661

def self.immature_peptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001063')
end

.immunoglobulin_region ⇒ Object

A region of immunoglobulin sequence, either constant or variable. (http://purl.obolibrary.org/obo/SO_0001832)

# File 'lib/biointerchange/so.rb', line 11197

def self.immunoglobulin_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001832')
end

.improved_high_quality_draft ⇒ Object

The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution. (http://purl.obolibrary.org/obo/SO_0001488)

# File 'lib/biointerchange/so.rb', line 9187

def self.improved_high_quality_draft
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001488')
end

.inactive_catalytic_site ⇒ Object

A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001618)

# File 'lib/biointerchange/so.rb', line 9949

def self.inactive_catalytic_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001618')
end

.inactive_ligand_binding_site ⇒ Object

A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001560)

# File 'lib/biointerchange/so.rb', line 9619

def self.inactive_ligand_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001560')
end

.incomplete_terminal_codon_variant ⇒ Object

A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed. (http://purl.obolibrary.org/obo/SO_0001626)

# File 'lib/biointerchange/so.rb', line 9991

def self.incomplete_terminal_codon_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001626')
end

.increased_polyadenylation_variant ⇒ Object

A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference. (http://purl.obolibrary.org/obo/SO_0001802)

# File 'lib/biointerchange/so.rb', line 11017

def self.increased_polyadenylation_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001802')
end

.increased_transcript_level_variant ⇒ Object

A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001542)

# File 'lib/biointerchange/so.rb', line 9511

def self.increased_transcript_level_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001542')
end

.increased_transcript_stability_variant ⇒ Object

A sequence variant that increases transcript stability with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001548)

# File 'lib/biointerchange/so.rb', line 9547

def self.increased_transcript_stability_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001548')
end

.increased_transcription_rate_variant ⇒ Object

A sequence variant that increases the rate of transcription with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001551)

# File 'lib/biointerchange/so.rb', line 9565

def self.increased_transcription_rate_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001551')
end

.increased_translational_product_level ⇒ Object

A sequence variant which increases the translational product level with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001556)

# File 'lib/biointerchange/so.rb', line 9595

def self.increased_translational_product_level
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001556')
end

.indel ⇒ Object

A sequence alteration which included an insertion and a deletion, affecting 2 or more bases. (http://purl.obolibrary.org/obo/SO_1000032)

# File 'lib/biointerchange/so.rb', line 12635

def self.indel
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000032')
end

.independently_known ⇒ Object

Attribute to describe a feature that is independently known - not predicted. (http://purl.obolibrary.org/obo/SO_0000906)

# File 'lib/biointerchange/so.rb', line 5717

def self.independently_known
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000906')
end

.inframe ⇒ Object

An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3. (http://purl.obolibrary.org/obo/SO_0001817)

# File 'lib/biointerchange/so.rb', line 11107

def self.inframe
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001817')
end

.inframe_deletion ⇒ Object

An inframe non synonymous variant that deletes bases from the coding sequence. (http://purl.obolibrary.org/obo/SO_0001822)

# File 'lib/biointerchange/so.rb', line 11137

def self.inframe_deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001822')
end

.inframe_indel ⇒ Object

A coding sequence variant where the change does not alter the frame of the transcript. (http://purl.obolibrary.org/obo/SO_0001820)

# File 'lib/biointerchange/so.rb', line 11125

def self.inframe_indel
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001820')
end

.inframe_insertion ⇒ Object

An inframe non synonymous variant that inserts bases into in the coding sequence. (http://purl.obolibrary.org/obo/SO_0001821)

# File 'lib/biointerchange/so.rb', line 11131

def self.inframe_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001821')
end

.inframe_variant ⇒ Object

A sequence variant which does not cause a disruption of the translational reading frame. (http://purl.obolibrary.org/obo/SO_0001650)

# File 'lib/biointerchange/so.rb', line 10123

def self.inframe_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001650')
end

.initiator_codon_variant ⇒ Object

A codon variant that changes at least one base of the first codon of a transcript. (http://purl.obolibrary.org/obo/SO_0001582)

# File 'lib/biointerchange/so.rb', line 9745

def self.initiator_codon_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001582')
end

.inosine ⇒ Object

A modified RNA base in which hypoxanthine is bound to the ribose ring. (http://purl.obolibrary.org/obo/SO_0001230)

# File 'lib/biointerchange/so.rb', line 7651

def self.inosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001230')
end

.INR1_motif ⇒ Object

A promoter motif with consensus sequence TCATTCG. (http://purl.obolibrary.org/obo/SO_0001163)

# File 'lib/biointerchange/so.rb', line 7249

def self.INR1_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001163')
end

.INR_motif ⇒ Object

A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element. (http://purl.obolibrary.org/obo/SO_0000014)

# File 'lib/biointerchange/so.rb', line 399

def self.INR_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000014')
end

.insert ⇒ Object

To insert a subsection of sequence. (http://purl.obolibrary.org/obo/SO_0000046)

# File 'lib/biointerchange/so.rb', line 585

def self.insert
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000046')
end

.insert_AA ⇒ Object

An edit to insert a AA dinucleotide. (http://purl.obolibrary.org/obo/SO_0000928)

# File 'lib/biointerchange/so.rb', line 5849

def self.insert_AA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000928')
end

.insert_AU ⇒ Object

An edit to insert a AU dinucleotide. (http://purl.obolibrary.org/obo/SO_0000927)

# File 'lib/biointerchange/so.rb', line 5843

def self.insert_AU
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000927')
end

.insert_C ⇒ Object

An edit to insert a cytidine. (http://purl.obolibrary.org/obo/SO_0000920)

# File 'lib/biointerchange/so.rb', line 5801

def self.insert_C
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000920')
end

.insert_CU ⇒ Object

An edit to insert a CU dinucleotide. (http://purl.obolibrary.org/obo/SO_0000926)

# File 'lib/biointerchange/so.rb', line 5837

def self.insert_CU
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000926')
end

.insert_dinucleotide ⇒ Object

An edit to insert a dinucleotide. (http://purl.obolibrary.org/obo/SO_0000921)

# File 'lib/biointerchange/so.rb', line 5807

def self.insert_dinucleotide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000921')
end

.insert_G ⇒ Object

An edit to insert a G. (http://purl.obolibrary.org/obo/SO_0000923)

# File 'lib/biointerchange/so.rb', line 5819

def self.insert_G
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000923')
end

.insert_GC ⇒ Object

An edit to insert a GC dinucleotide. (http://purl.obolibrary.org/obo/SO_0000924)

# File 'lib/biointerchange/so.rb', line 5825

def self.insert_GC
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000924')
end

.insert_GU ⇒ Object

An edit to insert a GU dinucleotide. (http://purl.obolibrary.org/obo/SO_0000925)

# File 'lib/biointerchange/so.rb', line 5831

def self.insert_GU
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000925')
end

.insert_U ⇒ Object

An edit to insert a U. (http://purl.obolibrary.org/obo/SO_0000917)

# File 'lib/biointerchange/so.rb', line 5783

def self.insert_U
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000917')
end

.insertion ⇒ Object

The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. (http://purl.obolibrary.org/obo/SO_0000667)

# File 'lib/biointerchange/so.rb', line 4325

def self.insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000667')
end

.insertion_attribute ⇒ Object

A quality of a chromosomal insertion,. (http://purl.obolibrary.org/obo/SO_0001512)

# File 'lib/biointerchange/so.rb', line 9331

def self.insertion_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001512')
end

.insertion_breakpoint ⇒ Object

The point within a chromosome where a insertion begins or ends. (http://purl.obolibrary.org/obo/SO_0001414)

# File 'lib/biointerchange/so.rb', line 8749

def self.insertion_breakpoint
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001414')
end

.insertion_sequence ⇒ Object

A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats. (http://purl.obolibrary.org/obo/SO_0000973)

# File 'lib/biointerchange/so.rb', line 6119

def self.insertion_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000973')
end

.insertion_site ⇒ Object

The junction where an insertion occurred. (http://purl.obolibrary.org/obo/SO_0000366)

# File 'lib/biointerchange/so.rb', line 2511

def self.insertion_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000366')
end

.insertional ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001522)

# File 'lib/biointerchange/so.rb', line 9391

def self.insertional
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001522')
end

.insertional_duplication ⇒ Object

A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication). (http://purl.obolibrary.org/obo/SO_1000154)

# File 'lib/biointerchange/so.rb', line 13259

def self.insertional_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000154')
end

.inside_intron ⇒ Object

An attribute to describe a gene when it is located within the intron of another gene. (http://purl.obolibrary.org/obo/SO_0000069)

# File 'lib/biointerchange/so.rb', line 731

def self.inside_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000069')
end

.inside_intron_antiparallel ⇒ Object

An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand. (http://purl.obolibrary.org/obo/SO_0000070)

# File 'lib/biointerchange/so.rb', line 737

def self.inside_intron_antiparallel
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000070')
end

.inside_intron_parallel ⇒ Object

An attribute to describe a gene when it is located within the intron of another gene and on the same strand. (http://purl.obolibrary.org/obo/SO_0000071)

# File 'lib/biointerchange/so.rb', line 743

def self.inside_intron_parallel
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000071')
end

.insulator ⇒ Object

A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression. (http://purl.obolibrary.org/obo/SO_0000627)

# File 'lib/biointerchange/so.rb', line 4085

def self.insulator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000627')
end

.insulator_binding_site ⇒ Object

A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. (http://purl.obolibrary.org/obo/SO_0001460)

# File 'lib/biointerchange/so.rb', line 9019

def self.insulator_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001460')
end

.integral_part_of ⇒ Object

X integral_part_of Y if and only if: X part_of Y and Y has_part X. (http://purl.obolibrary.org/obo/so_2_5_2.obo#integral_part_of)

# File 'lib/biointerchange/so.rb', line 155

def self.integral_part_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#integral_part_of')
end

.integrase_coding_region ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000369)

# File 'lib/biointerchange/so.rb', line 2529

def self.integrase_coding_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000369')
end

.integrated_mobile_genetic_element ⇒ Object

An MGE that is integrated into the host chromosome. (http://purl.obolibrary.org/obo/SO_0001039)

# File 'lib/biointerchange/so.rb', line 6509

def self.integrated_mobile_genetic_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001039')
end

.integrated_plasmid ⇒ Object

A plasmid sequence that is integrated within the host chromosome. (http://purl.obolibrary.org/obo/SO_0001040)

# File 'lib/biointerchange/so.rb', line 6515

def self.integrated_plasmid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001040')
end

.integration_excision_site ⇒ Object

A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site. (http://purl.obolibrary.org/obo/SO_0000946)

# File 'lib/biointerchange/so.rb', line 5957

def self.integration_excision_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000946')
end

.integron ⇒ Object

A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site. (http://purl.obolibrary.org/obo/SO_0000365)

# File 'lib/biointerchange/so.rb', line 2505

def self.integron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000365')
end

.intein ⇒ Object

A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond. (http://purl.obolibrary.org/obo/SO_0000728)

# File 'lib/biointerchange/so.rb', line 4691

def self.intein
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000728')
end

.intein_containing ⇒ Object

An attribute of protein-coding genes where the initial protein product contains an intein. (http://purl.obolibrary.org/obo/SO_0000729)

# File 'lib/biointerchange/so.rb', line 4697

def self.intein_containing
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000729')
end

.interband ⇒ Object

A light region between two darkly staining bands in a polytene chromosome. (http://purl.obolibrary.org/obo/SO_0000450)

# File 'lib/biointerchange/so.rb', line 3019

def self.interband
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000450')
end

.interchromosomal ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001511)

# File 'lib/biointerchange/so.rb', line 9325

def self.interchromosomal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001511')
end

.interchromosomal_breakpoint ⇒ Object

A rearrangement breakpoint between two different chromosomes. (http://purl.obolibrary.org/obo/SO_0001873)

# File 'lib/biointerchange/so.rb', line 11443

def self.interchromosomal_breakpoint
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001873')
end

.interchromosomal_duplication ⇒ Object

A chromosome duplication involving an insertion from another chromosome. (http://purl.obolibrary.org/obo/SO_0000457)

# File 'lib/biointerchange/so.rb', line 3061

def self.interchromosomal_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000457')
end

.interchromosomal_mutation ⇒ Object

A chromosomal structure variation whereby more than one chromosome is involved. (http://purl.obolibrary.org/obo/SO_1000031)

# File 'lib/biointerchange/so.rb', line 12629

def self.interchromosomal_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000031')
end

.interchromosomal_transposition ⇒ Object

A chromosome structure variation whereby a transposition occurred between chromosomes. (http://purl.obolibrary.org/obo/SO_1000155)

# File 'lib/biointerchange/so.rb', line 13265

def self.interchromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000155')
end

.intergenic_region ⇒ Object

A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome. (http://purl.obolibrary.org/obo/SO_0000605)

# File 'lib/biointerchange/so.rb', line 3953

def self.intergenic_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000605')
end

.intergenic_variant ⇒ Object

A sequence variant located in the intergenic region, between genes. (http://purl.obolibrary.org/obo/SO_0001628)

# File 'lib/biointerchange/so.rb', line 10003

def self.intergenic_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001628')
end

.interior_coding_exon ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000004)

# File 'lib/biointerchange/so.rb', line 339

def self.interior_coding_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000004')
end

.interior_exon ⇒ Object

An exon that is bounded by 5' and 3' splice sites. (http://purl.obolibrary.org/obo/SO_0000201)

# File 'lib/biointerchange/so.rb', line 1527

def self.interior_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000201')
end

.interior_intron ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000191)

# File 'lib/biointerchange/so.rb', line 1467

def self.interior_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000191')
end

.intermediate ⇒ Object

An attribute to describe a feature between stages of processing. (http://purl.obolibrary.org/obo/SO_0000933)

# File 'lib/biointerchange/so.rb', line 5879

def self.intermediate
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000933')
end

.intermediate_element ⇒ Object

A core promoter region of RNA polymerase III type 1 promoters. (http://purl.obolibrary.org/obo/SO_0001677)

# File 'lib/biointerchange/so.rb', line 10273

def self.intermediate_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001677')
end

.internal_eliminated_sequence ⇒ Object

A sequence eliminated from the genome of ciliates during nuclear differentiation. (http://purl.obolibrary.org/obo/SO_0000671)

# File 'lib/biointerchange/so.rb', line 4349

def self.internal_eliminated_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000671')
end

.internal_feature_elongation ⇒ Object

A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence. (http://purl.obolibrary.org/obo/SO_0001908)

# File 'lib/biointerchange/so.rb', line 11653

def self.internal_feature_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001908')
end

.internal_guide_sequence ⇒ Object

A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity. (http://purl.obolibrary.org/obo/SO_0001016)

# File 'lib/biointerchange/so.rb', line 6371

def self.internal_guide_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001016')
end

.internal_ribosome_entry_site ⇒ Object

Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation. (http://purl.obolibrary.org/obo/SO_0000243)

# File 'lib/biointerchange/so.rb', line 1779

def self.internal_ribosome_entry_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000243')
end

.internal_Shine_Dalgarno_sequence ⇒ Object

A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria. (http://purl.obolibrary.org/obo/SO_1001260)

# File 'lib/biointerchange/so.rb', line 13505

def self.internal_Shine_Dalgarno_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001260')
end

.internal_transcribed_spacer_region ⇒ Object

Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs. (http://purl.obolibrary.org/obo/SO_0000639)

# File 'lib/biointerchange/so.rb', line 4157

def self.internal_transcribed_spacer_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000639')
end

.internal_UTR ⇒ Object

A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal. (http://purl.obolibrary.org/obo/SO_0000241)

# File 'lib/biointerchange/so.rb', line 1767

def self.internal_UTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000241')
end

.intrachromosomal ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001510)

# File 'lib/biointerchange/so.rb', line 9319

def self.intrachromosomal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001510')
end

.intrachromosomal_breakpoint ⇒ Object

A rearrangement breakpoint within the same chromosome. (http://purl.obolibrary.org/obo/SO_0001874)

# File 'lib/biointerchange/so.rb', line 11449

def self.intrachromosomal_breakpoint
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001874')
end

.intrachromosomal_duplication ⇒ Object

A duplication that occurred within a chromosome. (http://purl.obolibrary.org/obo/SO_1000038)

# File 'lib/biointerchange/so.rb', line 12659

def self.intrachromosomal_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000038')
end

.intrachromosomal_mutation ⇒ Object

A chromosomal structure variation within a single chromosome. (http://purl.obolibrary.org/obo/SO_1000028)

# File 'lib/biointerchange/so.rb', line 12611

def self.intrachromosomal_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000028')
end

.intrachromosomal_transposition ⇒ Object

A chromosome structure variation whereby a transposition occurred within a chromosome. (http://purl.obolibrary.org/obo/SO_1000041)

# File 'lib/biointerchange/so.rb', line 12677

def self.intrachromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000041')
end

.intramembrane_polypeptide_region ⇒ Object

Polypeptide region present in the lipid bilayer. (http://purl.obolibrary.org/obo/SO_0001075)

# File 'lib/biointerchange/so.rb', line 6721

def self.intramembrane_polypeptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001075')
end

.intrinsically_unstructured_polypeptide_region ⇒ Object

A region of polypeptide chain with high conformational flexibility. (http://purl.obolibrary.org/obo/SO_0100003)

# File 'lib/biointerchange/so.rb', line 12365

def self.intrinsically_unstructured_polypeptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100003')
end

.introgressed_chromosome_region ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000664)

# File 'lib/biointerchange/so.rb', line 4307

def self.introgressed_chromosome_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000664')
end

.intron ⇒ Object

A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it. (http://purl.obolibrary.org/obo/SO_0000188)

# File 'lib/biointerchange/so.rb', line 1449

def self.intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000188')
end

.intron_attribute ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000661)

# File 'lib/biointerchange/so.rb', line 4289

def self.intron_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000661')
end

.intron_base_5 ⇒ Object

Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron. (http://purl.obolibrary.org/obo/SO_0001994)

# File 'lib/biointerchange/so.rb', line 12167

def self.intron_base_5
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001994')
end

.intron_domain ⇒ Object

Requested by Colin Batchelor, Feb 2007. (http://purl.obolibrary.org/obo/SO_0001014)

# File 'lib/biointerchange/so.rb', line 6359

def self.intron_domain
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001014')
end

.intron_gain ⇒ Object

A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor. (http://purl.obolibrary.org/obo/SO_0001573)

# File 'lib/biointerchange/so.rb', line 9697

def self.intron_gain
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001573')
end

.intron_variant ⇒ Object

A transcript variant occurring within an intron. (http://purl.obolibrary.org/obo/SO_0001627)

# File 'lib/biointerchange/so.rb', line 9997

def self.intron_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001627')
end

.intronic_lncRNA ⇒ Object

A lnc_RNA totally contained within an intron. (http://purl.obolibrary.org/obo/SO_0001903)

# File 'lib/biointerchange/so.rb', line 11623

def self.intronic_lncRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001903')
end

.intronic_regulatory_region ⇒ Object

A regulatory region that is part of an intron. (http://purl.obolibrary.org/obo/SO_0001492)

# File 'lib/biointerchange/so.rb', line 9211

def self.intronic_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001492')
end

.intronic_splice_enhancer ⇒ Object

Sequences within the intron that modulate splice site selection for some introns. (http://purl.obolibrary.org/obo/SO_0000320)

# File 'lib/biointerchange/so.rb', line 2241

def self.intronic_splice_enhancer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000320')
end

.invalidated ⇒ Object

An attribute describing a feature that is invalidated. (http://purl.obolibrary.org/obo/SO_0000790)

# File 'lib/biointerchange/so.rb', line 5057

def self.invalidated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000790')
end

.invalidated_by_chimeric_cDNA ⇒ Object

A cDNA clone constructed from more than one mRNA. Usually an experimental artifact. (http://purl.obolibrary.org/obo/SO_0000362)

# File 'lib/biointerchange/so.rb', line 2487

def self.invalidated_by_chimeric_cDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000362')
end

.invalidated_by_genomic_contamination ⇒ Object

An attribute to describe a feature that is invalidated due to genomic contamination. (http://purl.obolibrary.org/obo/SO_0000414)

# File 'lib/biointerchange/so.rb', line 2799

def self.invalidated_by_genomic_contamination
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000414')
end

.invalidated_by_genomic_polyA_primed_cDNA ⇒ Object

An attribute to describe a feature that is invalidated due to polyA priming. (http://purl.obolibrary.org/obo/SO_0000415)

# File 'lib/biointerchange/so.rb', line 2805

def self.invalidated_by_genomic_polyA_primed_cDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000415')
end

.invalidated_by_partial_processing ⇒ Object

An attribute to describe a feature that is invalidated due to partial processing. (http://purl.obolibrary.org/obo/SO_0000416)

# File 'lib/biointerchange/so.rb', line 2811

def self.invalidated_by_partial_processing
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000416')
end

.invalidated_cDNA_clone ⇒ Object

A cDNA clone that is invalid. (http://purl.obolibrary.org/obo/SO_0000809)

# File 'lib/biointerchange/so.rb', line 5147

def self.invalidated_cDNA_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000809')
end

.inversion ⇒ Object

A continuous nucleotide sequence is inverted in the same position. (http://purl.obolibrary.org/obo/SO_1000036)

# File 'lib/biointerchange/so.rb', line 12647

def self.inversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000036')
end

.inversion_attribute ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001517)

# File 'lib/biointerchange/so.rb', line 9361

def self.inversion_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001517')
end

.inversion_breakpoint ⇒ Object

The point within a chromosome where an inversion begins or ends. (http://purl.obolibrary.org/obo/SO_0001022)

# File 'lib/biointerchange/so.rb', line 6407

def self.inversion_breakpoint
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001022')
end

.inversion_cum_translocation ⇒ Object

A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break. (http://purl.obolibrary.org/obo/SO_1000148)

# File 'lib/biointerchange/so.rb', line 13223

def self.inversion_cum_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000148')
end

.inversion_derived_aneuploid_chromosome ⇒ Object

A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion. (http://purl.obolibrary.org/obo/SO_0000567)

# File 'lib/biointerchange/so.rb', line 3725

def self.inversion_derived_aneuploid_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000567')
end

.inversion_derived_bipartite_deficiency ⇒ Object

A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion. (http://purl.obolibrary.org/obo/SO_0000461)

# File 'lib/biointerchange/so.rb', line 3085

def self.inversion_derived_bipartite_deficiency
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000461')
end

.inversion_derived_bipartite_duplication ⇒ Object

A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion. (http://purl.obolibrary.org/obo/SO_0000547)

# File 'lib/biointerchange/so.rb', line 3601

def self.inversion_derived_bipartite_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000547')
end

.inversion_derived_deficiency_plus_aneuploid ⇒ Object

A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion. (http://purl.obolibrary.org/obo/SO_0000512)

# File 'lib/biointerchange/so.rb', line 3391

def self.inversion_derived_deficiency_plus_aneuploid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000512')
end

.inversion_derived_deficiency_plus_duplication ⇒ Object

A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion. (http://purl.obolibrary.org/obo/SO_0000465)

# File 'lib/biointerchange/so.rb', line 3109

def self.inversion_derived_deficiency_plus_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000465')
end

.inversion_derived_duplication_plus_aneuploid ⇒ Object

A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion. (http://purl.obolibrary.org/obo/SO_0000549)

# File 'lib/biointerchange/so.rb', line 3613

def self.inversion_derived_duplication_plus_aneuploid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000549')
end

.inversion_site ⇒ Object

A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites. (http://purl.obolibrary.org/obo/SO_0000948)

# File 'lib/biointerchange/so.rb', line 5969

def self.inversion_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000948')
end

.inversion_site_part ⇒ Object

A region located within an inversion site. (http://purl.obolibrary.org/obo/SO_0001048)

# File 'lib/biointerchange/so.rb', line 6563

def self.inversion_site_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001048')
end

.invert ⇒ Object

To invert a subsection of sequence. (http://purl.obolibrary.org/obo/SO_0000047)

# File 'lib/biointerchange/so.rb', line 591

def self.invert
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000047')
end

.inverted ⇒ Object

A quality of an insertion where the insert is in a cytologically inverted orientation. (http://purl.obolibrary.org/obo/SO_0001515)

# File 'lib/biointerchange/so.rb', line 9349

def self.inverted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001515')
end

.inverted_insertional_duplication ⇒ Object

An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments. (http://purl.obolibrary.org/obo/SO_1000153)

# File 'lib/biointerchange/so.rb', line 13253

def self.inverted_insertional_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000153')
end

.inverted_interchromosomal_transposition ⇒ Object

An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment. (http://purl.obolibrary.org/obo/SO_1000156)

# File 'lib/biointerchange/so.rb', line 13271

def self.inverted_interchromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000156')
end

.inverted_intrachromosomal_transposition ⇒ Object

An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments. (http://purl.obolibrary.org/obo/SO_1000158)

# File 'lib/biointerchange/so.rb', line 13283

def self.inverted_intrachromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000158')
end

.inverted_repeat ⇒ Object

The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC. (http://purl.obolibrary.org/obo/SO_0000294)

# File 'lib/biointerchange/so.rb', line 2085

def self.inverted_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000294')
end

.inverted_ring_chromosome ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000439)

# File 'lib/biointerchange/so.rb', line 2953

def self.inverted_ring_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000439')
end

.inverted_tandem_duplication ⇒ Object

A tandem duplication where the individual regions are not in the same orientation. (http://purl.obolibrary.org/obo/SO_1000040)

# File 'lib/biointerchange/so.rb', line 12671

def self.inverted_tandem_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000040')
end

.IRLinv_site ⇒ Object

Component of the inversion site located at the left of a region susceptible to site-specific inversion. (http://purl.obolibrary.org/obo/SO_0001046)

# File 'lib/biointerchange/so.rb', line 6551

def self.IRLinv_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001046')
end

.iron_repressed_GATA_element ⇒ Object

A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron. (http://purl.obolibrary.org/obo/SO_0001851)

# File 'lib/biointerchange/so.rb', line 11311

def self.iron_repressed_GATA_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001851')
end

.iron_responsive_element ⇒ Object

A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins. (http://purl.obolibrary.org/obo/SO_0001182)

# File 'lib/biointerchange/so.rb', line 7363

def self.iron_responsive_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001182')
end

.IRRinv_site ⇒ Object

Component of the inversion site located at the right of a region susceptible to site-specific inversion. (http://purl.obolibrary.org/obo/SO_0001047)

# File 'lib/biointerchange/so.rb', line 6557

def self.IRRinv_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001047')
end

.is_class?(uri) ⇒ Boolean

Determines whether the given URI is a class.

uri

URI that is tested for being a class

Returns:

• (Boolean)

# File 'lib/biointerchange/so.rb', line 13847

def self.is_class?(uri)
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000000') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000001') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000002') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000003') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000004') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000005') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000006') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000007') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000008') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000009') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000010') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000011') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000012') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000013') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000014') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000015') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000016') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000017') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000018') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000020') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000021') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000022') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000023') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000024') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000025') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000026') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000027') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000028') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000029') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000030') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000031') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000032') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000033') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000034') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000035') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000036') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000037') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000038') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000039') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000040') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000041') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000042') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000043') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000044') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000045') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000046') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000047') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000048') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000049') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000050') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000051') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000052') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000053') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000054') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000055') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000056') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000057') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000058') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000059') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000060') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000061') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000062') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000063') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000064') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000065') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000066') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000067') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000068') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000069') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000070') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000071') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000072') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000073') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000074') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000075') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000076') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000077') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000078') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000079') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000080') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000081') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000082') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000083') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000084') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000085') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000086') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000087') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000088') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000089') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000090') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000091') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000092') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000093') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000094') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000095') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000096') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000097') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000098') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000099') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000100') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000101') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000102') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000103') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000104') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000105') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000106') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000107') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000108') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000109') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000110') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000111') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000112') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000113') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000114') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000115') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000116') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000117') then
    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000930') then
    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001117') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001118') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001119') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001120') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001121') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001122') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001123') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001124') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001125') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001126') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001127') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001128') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001129') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001130') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001131') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001132') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001133') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001134') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001135') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001136') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001137') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001138') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001139') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001140') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001141') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001142') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001143') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001144') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001145') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001146') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001147') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001148') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001149') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001150') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001151') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001152') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001153') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001154') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001155') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001156') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001157') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001158') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001159') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001160') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001161') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001162') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001163') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001164') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001165') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001166') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001167') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001168') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001169') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001170') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001171') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001172') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001173') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001174') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001175') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001176') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001177') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001178') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001179') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001180') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001181') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001182') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001183') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001184') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001185') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001186') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001187') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001188') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001189') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001190') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001191') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001192') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001193') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001194') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001195') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001196') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001197') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001198') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001202') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001203') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001204') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001205') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001206') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001210') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001212') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001216') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001218') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001220') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001221') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001222') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001223') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001224') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001225') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001226') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001250') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001251') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001252') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001253') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001254') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001255') then
    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001258') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001260') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001261') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001262') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001263') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001264') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001265') then
    return true
  end
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001270') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001272') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001273') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001274') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001275') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001277') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001278') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001279') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001280') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001281') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001282') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001283') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001284') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001285') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001286') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001287') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001288') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001289') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001290') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001291') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001292') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001293') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001294') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001295') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001296') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001297') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001298') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001299') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001300') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001301') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001302') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001303') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001304') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001305') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001306') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001307') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001308') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001309') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001310') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001311') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001312') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001313') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001314') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001315') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001316') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001318') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001319') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001320') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001321') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001322') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001323') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001324') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001325') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001326') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001327') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001328') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001329') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001330') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001331') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001332') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001333') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001334') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001335') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001336') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001337') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001338') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001339') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001340') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001342') then
    return true
  end
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001351') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001357') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001358') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001359') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001360') then
    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001363') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001364') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001365') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001366') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001367') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001368') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001369') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001370') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001375') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001376') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001377') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001378') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001379') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001384') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
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    return true
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    return true
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    return true
  end
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    return true
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    return true
  end
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    return true
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001516') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001518') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001519') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001520') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001521') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001522') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001523') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001524') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001525') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001526') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001527') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001528') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001529') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001530') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001532') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001533') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001534') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001535') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001536') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001537') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001538') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001539') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001540') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001551') then
    return true
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001553') then
    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001556') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001557') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001558') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001559') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001560') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001561') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001562') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001563') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001564') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001565') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001566') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001567') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001568') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001569') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001570') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001571') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001572') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001573') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001574') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001575') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001576') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001577') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001578') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001579') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001580') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001582') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001583') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001585') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001586') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001587') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001589') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001591') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001593') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001594') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001595') then
    return true
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001698') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001699') then
    return true
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    return true
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    return true
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001703') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001704') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001705') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001706') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001707') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001708') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001709') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001710') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001711') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001712') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001713') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001714') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001715') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001716') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001717') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001718') then
    return true
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001721') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001722') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001723') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001724') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001725') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001726') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001727') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001728') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001729') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001730') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001731') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001732') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001733') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001734') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001735') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001736') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001737') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001738') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001739') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001740') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001741') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001742') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001743') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001744') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001745') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001746') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001747') then
    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001750') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001751') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001752') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001753') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001754') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001755') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001756') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001757') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001758') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001759') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001760') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001761') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001762') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001763') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001764') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001765') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001766') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001767') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001768') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001769') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001770') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001771') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001772') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001773') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001774') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001775') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001776') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001777') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001778') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001779') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001780') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001781') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001782') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001784') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001785') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001786') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001787') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001788') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001789') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001790') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001791') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001792') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001793') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001794') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001795') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001796') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001797') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001798') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001799') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001800') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001801') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001802') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001803') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001804') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001805') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001806') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001807') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001808') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001809') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001810') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001812') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001813') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001814') then
    return true
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001816') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001817') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001818') then
    return true
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001820') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001822') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001824') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001825') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001827') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001828') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001829') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001830') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001832') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001834') then
    return true
  end
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    return true
  end
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    return true
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001838') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001840') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001842') then
    return true
  end
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    return true
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    return true
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    return true
  end
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    return true
  end
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    return true
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001851') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001852') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001856') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001857') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001858') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001860') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001861') then
    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001866') then
    return true
  end
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    return true
  end
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    return true
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  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001869') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001870') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001871') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001872') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001873') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001874') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001876') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001878') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001879') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001881') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001882') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001883') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001884') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001885') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001886') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001887') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001888') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001889') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001891') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001892') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001893') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001894') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001896') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001897') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001898') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001899') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001900') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001901') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001902') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001903') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001904') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001905') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001906') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001907') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001908') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001909') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001910') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001911') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001912') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001913') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001914') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001915') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001916') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001917') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001918') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001919') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001920') then
    return true
  end
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    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001922') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001923') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001924') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001925') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001926') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001927') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001928') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001929') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001930') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001931') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001932') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001933') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001934') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001935') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001936') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001937') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001938') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001939') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001940') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001941') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001942') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001943') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001944') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001945') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001946') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001947') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001948') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001949') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001950') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001951') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001952') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001953') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001954') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001955') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001956') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001957') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001958') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001959') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001960') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001961') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001962') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001963') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001964') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001965') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001966') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001967') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001968') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001969') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001970') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001971') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001972') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001973') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001974') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001975') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001976') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001977') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001978') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001979') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001980') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001981') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001982') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001983') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001984') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001985') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001986') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001987') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001988') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001989') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001990') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001991') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001992') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001993') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001994') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001995') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001996') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001997') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001998') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001999') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002000') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002001') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002002') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002003') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002004') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002005') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002006') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002007') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005836') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005837') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005841') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005843') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005845') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005847') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005848') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005849') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005850') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005851') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005852') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005853') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005854') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005855') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005856') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005857') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005858') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100001') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100002') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100003') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100004') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100005') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100006') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100007') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100008') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100009') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100010') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100011') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100012') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100013') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100014') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100015') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100016') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100017') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100018') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100019') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100020') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100021') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000002') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000005') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000008') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000009') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000010') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000011') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000012') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000013') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000014') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000015') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000016') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000017') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000018') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000019') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000020') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000021') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000022') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000023') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000024') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000025') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000026') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000027') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000028') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000029') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000030') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000031') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000032') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000035') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000036') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000037') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000038') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000039') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000040') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000041') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000042') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000043') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000044') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000045') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000046') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000047') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000048') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000049') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000050') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000054') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000055') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000056') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000057') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000058') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000059') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000060') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000061') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000062') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000063') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000064') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000065') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000066') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000067') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000068') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000069') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000070') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000071') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000072') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000073') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000074') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000075') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000076') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000078') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000079') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000080') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000081') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000082') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000083') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000084') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000085') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000086') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000087') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000088') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000089') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000092') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000093') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000094') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000095') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000096') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000097') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000098') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000099') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000100') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000101') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000102') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000103') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000104') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000105') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000106') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000107') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000108') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000109') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000110') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000111') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000112') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000115') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000116') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000117') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000118') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000119') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000120') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000121') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000122') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000123') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000124') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000125') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000126') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000127') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000132') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000134') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000136') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000138') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000140') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000141') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000142') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000143') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000144') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000145') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000146') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000147') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000148') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000149') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000150') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000151') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000152') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000153') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000154') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000155') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000156') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000157') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000158') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000159') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000160') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000161') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000162') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000170') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000171') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000173') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000175') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000180') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000181') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000182') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000183') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000184') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000185') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000186') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001186') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001187') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001188') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001189') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001190') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001191') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001192') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001193') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001194') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001195') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001196') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001197') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001217') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001244') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001246') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001247') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001249') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001251') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001254') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001255') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001259') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001260') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001261') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001262') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001263') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001264') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001265') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001266') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001267') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001268') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001269') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001270') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001271') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001272') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001273') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001274') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001275') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001277') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001279') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001280') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001281') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001282') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001283') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001284') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001285') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001286') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001287') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001288') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_2000061') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_3000000') then
    return true
  end
  return false
end

.is_consecutive_sequence_of ⇒ Object

R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical). (http://purl.obolibrary.org/obo/so_2_5_2.obo#is_consecutive_sequence_of)

# File 'lib/biointerchange/so.rb', line 161

def self.is_consecutive_sequence_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#is_consecutive_sequence_of')
end

.is_datatype_property?(uri) ⇒ Boolean

Determines whether the given URI is a datatype property.

uri

URI that is tested for being a datatype property

Returns:

• (Boolean)

# File 'lib/biointerchange/so.rb', line 13840

def self.is_datatype_property?(uri)
  return false
end

.is_named_individual?(uri) ⇒ Boolean

Determines whether the given URI is a named individual.

uri

URI that is tested for being a named individual

Returns:

• (Boolean)

# File 'lib/biointerchange/so.rb', line 20544

def self.is_named_individual?(uri)
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/anonymous#variant_of') then
    return true
  end
  return false
end

.is_object_property?(uri) ⇒ Boolean

Determines whether the given URI is an object property.

uri

URI that is tested for being an object property

Returns:

• (Boolean)

# File 'lib/biointerchange/so.rb', line 13680

def self.is_object_property?(uri)
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/part_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#adjacent_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#associated_with') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#complete_evidence_for_feature') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#connects_on') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#contained_by') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#contains') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#derives_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#disconnected_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#edited_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#edited_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#evidence_for_feature') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#exemplar_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#finished_by') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#finishes') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#gained') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#genome_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#guided_by') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#guides') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#has_integral_part') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#has_origin') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#has_part') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#has_quality') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#homologous_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#integral_part_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#is_consecutive_sequence_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#lost') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#maximally_overlaps') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#member_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#non_functional_homolog_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#orthologous_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#overlaps') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#paralogous_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#part_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#partial_evidence_for_feature') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#position_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#processed_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#processed_into') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#recombined_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#recombined_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#sequence_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#similar_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#started_by') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#starts') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#trans_spliced_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#trans_spliced_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#transcribed_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#transcribed_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#translates_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#translation_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#variant_of') then
    return true
  end
  return false
end

.isoleucine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001438)

# File 'lib/biointerchange/so.rb', line 8887

def self.isoleucine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001438')
end

.isoleucine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding isoleucyl tRNA (SO:0000263). (http://purl.obolibrary.org/obo/SO_0000220)

# File 'lib/biointerchange/so.rb', line 1641

def self.isoleucine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000220')
end

.isoleucyl_tRNA ⇒ Object

A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region. (http://purl.obolibrary.org/obo/SO_0000263)

# File 'lib/biointerchange/so.rb', line 1899

def self.isoleucyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000263')
end

.isowyosine ⇒ Object

Isowyosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001342)

# File 'lib/biointerchange/so.rb', line 8317

def self.isowyosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001342')
end

.ISRE ⇒ Object

An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding. (http://purl.obolibrary.org/obo/SO_0001715)

# File 'lib/biointerchange/so.rb', line 10501

def self.ISRE
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001715')
end

.J_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000511)

# File 'lib/biointerchange/so.rb', line 3385

def self.J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000511')
end

.J_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene. (http://purl.obolibrary.org/obo/SO_0000513)

# File 'lib/biointerchange/so.rb', line 3397

def self.J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000513')
end

.J_gene_recombination_feature ⇒ Object

Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence. (http://purl.obolibrary.org/obo/SO_0000302)

# File 'lib/biointerchange/so.rb', line 2133

def self.J_gene_recombination_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000302')
end

.J_gene_segment ⇒ Object

Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment. (http://purl.obolibrary.org/obo/SO_0000470)

# File 'lib/biointerchange/so.rb', line 3139

def self.J_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000470')
end

.J_heptamer ⇒ Object

7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. (http://purl.obolibrary.org/obo/SO_0000515)

# File 'lib/biointerchange/so.rb', line 3409

def self.J_heptamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000515')
end

.J_nonamer ⇒ Object

9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. (http://purl.obolibrary.org/obo/SO_0000514)

# File 'lib/biointerchange/so.rb', line 3403

def self.J_nonamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000514')
end

.J_spacer ⇒ Object

12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. (http://purl.obolibrary.org/obo/SO_0000517)

# File 'lib/biointerchange/so.rb', line 3421

def self.J_spacer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000517')
end

.junction ⇒ Object

A sequence_feature with an extent of zero. (http://purl.obolibrary.org/obo/SO_0000699)

# File 'lib/biointerchange/so.rb', line 4517

def self.junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000699')
end

.K_turn_RNA_motif ⇒ Object

The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices. (http://purl.obolibrary.org/obo/SO_0000023)

# File 'lib/biointerchange/so.rb', line 447

def self.K_turn_RNA_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000023')
end

.KEN_box ⇒ Object

A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN. (http://purl.obolibrary.org/obo/SO_0001807)

# File 'lib/biointerchange/so.rb', line 11047

def self.KEN_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001807')
end

.kinetoplast ⇒ Object

A kinetoplast is an interlocked network of thousands of minicircles and tens of maxi circles, located near the base of the flagellum of some protozoan species. (http://purl.obolibrary.org/obo/SO_0000741)

# File 'lib/biointerchange/so.rb', line 4769

def self.kinetoplast
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000741')
end

.kinetoplast_gene ⇒ Object

A gene located in kinetoplast sequence. (http://purl.obolibrary.org/obo/SO_0000089)

# File 'lib/biointerchange/so.rb', line 851

def self.kinetoplast_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000089')
end

.kozak_sequence ⇒ Object

A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence. (http://purl.obolibrary.org/obo/SO_0001647)

# File 'lib/biointerchange/so.rb', line 10117

def self.kozak_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001647')
end

.L_box ⇒ Object

An orientation dependent regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants. (http://purl.obolibrary.org/obo/SO_0001981)

# File 'lib/biointerchange/so.rb', line 12089

def self.L_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001981')
end

.laevosynaptic_chromosome ⇒ Object

LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres. (http://purl.obolibrary.org/obo/SO_1000143)

# File 'lib/biointerchange/so.rb', line 13193

def self.laevosynaptic_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000143')
end

.lambda_clone ⇒ Object

A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome. (http://purl.obolibrary.org/obo/SO_0000160)

# File 'lib/biointerchange/so.rb', line 1277

def self.lambda_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000160')
end

.lambda_vector ⇒ Object

The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome. (http://purl.obolibrary.org/obo/SO_0000754)

# File 'lib/biointerchange/so.rb', line 4847

def self.lambda_vector
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000754')
end

.large_subunit_rRNA ⇒ Object

Ribosomal RNA transcript that structures the large subunit of the ribosome. (http://purl.obolibrary.org/obo/SO_0000651)

# File 'lib/biointerchange/so.rb', line 4229

def self.large_subunit_rRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000651')
end

.lariat_intron ⇒ Object

A kind of intron whereby the excision is driven by lariat formation. (http://purl.obolibrary.org/obo/SO_0001958)

# File 'lib/biointerchange/so.rb', line 11957

def self.lariat_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001958')
end

.left_handed_peptide_helix ⇒ Object

A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw. (http://purl.obolibrary.org/obo/SO_0001115)

# File 'lib/biointerchange/so.rb', line 6961

def self.left_handed_peptide_helix
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001115')
end

.lethal_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001773)

# File 'lib/biointerchange/so.rb', line 10849

def self.lethal_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001773')
end

.leucine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001437)

# File 'lib/biointerchange/so.rb', line 8881

def self.leucine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001437')
end

.leucine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding leucyl tRNA (SO:0000264). (http://purl.obolibrary.org/obo/SO_0000221)

# File 'lib/biointerchange/so.rb', line 1647

def self.leucine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000221')
end

.leucoplast_chromosome ⇒ Object

A chromosome with origin in a leucoplast. (http://purl.obolibrary.org/obo/SO_0000823)

# File 'lib/biointerchange/so.rb', line 5231

def self.leucoplast_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000823')
end

.leucoplast_gene ⇒ Object

A plastid gene from leucoplast sequence. (http://purl.obolibrary.org/obo/SO_0000095)

# File 'lib/biointerchange/so.rb', line 887

def self.leucoplast_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000095')
end

.leucoplast_sequence ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000747)

# File 'lib/biointerchange/so.rb', line 4805

def self.leucoplast_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000747')
end

.leucyl_tRNA ⇒ Object

A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region. (http://purl.obolibrary.org/obo/SO_0000264)

# File 'lib/biointerchange/so.rb', line 1905

def self.leucyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000264')
end

.level_of_transcript_variant ⇒ Object

A sequence variant which alters the level of a transcript. (http://purl.obolibrary.org/obo/SO_0001540)

# File 'lib/biointerchange/so.rb', line 9499

def self.level_of_transcript_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001540')
end

.ligand_binding_site ⇒ Object

A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone. (http://purl.obolibrary.org/obo/SO_0001657)

# File 'lib/biointerchange/so.rb', line 10153

def self.ligand_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001657')
end

.ligation_based_read ⇒ Object

A read produced by ligation based sequencing technologies. (http://purl.obolibrary.org/obo/SO_0001425)

# File 'lib/biointerchange/so.rb', line 8815

def self.ligation_based_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001425')
end

.lincRNA ⇒ Object

A multiexonic non-coding RNA transcribed by RNA polymerase II. (http://purl.obolibrary.org/obo/SO_0001463)

# File 'lib/biointerchange/so.rb', line 9037

def self.lincRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001463')
end

.lincRNA_gene ⇒ Object

A gene that encodes large intervening non-coding RNA. (http://purl.obolibrary.org/obo/SO_0001641)

# File 'lib/biointerchange/so.rb', line 10081

def self.lincRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001641')
end

.LINE_element ⇒ Object

A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats. (http://purl.obolibrary.org/obo/SO_0000194)

# File 'lib/biointerchange/so.rb', line 1485

def self.LINE_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000194')
end

.linear ⇒ Object

A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue. (http://purl.obolibrary.org/obo/SO_0000987)

# File 'lib/biointerchange/so.rb', line 6197

def self.linear
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000987')
end

.linear_double_stranded_DNA_chromosome ⇒ Object

Structural unit composed of a self-replicating, double-stranded, linear DNA molecule. (http://purl.obolibrary.org/obo/SO_0000957)

# File 'lib/biointerchange/so.rb', line 6023

def self.linear_double_stranded_DNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000957')
end

.linear_double_stranded_RNA_chromosome ⇒ Object

Structural unit composed of a self-replicating, double-stranded, linear RNA molecule. (http://purl.obolibrary.org/obo/SO_0000964)

# File 'lib/biointerchange/so.rb', line 6065

def self.linear_double_stranded_RNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000964')
end

.linear_single_stranded_DNA_chromosome ⇒ Object

Structural unit composed of a self-replicating, single-stranded, linear DNA molecule. (http://purl.obolibrary.org/obo/SO_0000959)

# File 'lib/biointerchange/so.rb', line 6035

def self.linear_single_stranded_DNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000959')
end

.linear_single_stranded_RNA_chromosome ⇒ Object

Structural unit composed of a self-replicating, single-stranded, linear RNA molecule. (http://purl.obolibrary.org/obo/SO_0000963)

# File 'lib/biointerchange/so.rb', line 6059

def self.linear_single_stranded_RNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000963')
end

.linkage_group ⇒ Object

A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned. (http://purl.obolibrary.org/obo/SO_0000018)

# File 'lib/biointerchange/so.rb', line 423

def self.linkage_group
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000018')
end

.lipoprotein_signal_peptide ⇒ Object

A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes. (http://purl.obolibrary.org/obo/SO_0100009)

# File 'lib/biointerchange/so.rb', line 12401

def self.lipoprotein_signal_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100009')
end

.LNA ⇒ Object

An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link. (http://purl.obolibrary.org/obo/SO_0001188)

# File 'lib/biointerchange/so.rb', line 7399

def self.LNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001188')
end

.LNA_oligo ⇒ Object

An oligo composed of LNA residues. (http://purl.obolibrary.org/obo/SO_0001189)

# File 'lib/biointerchange/so.rb', line 7405

def self.LNA_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001189')
end

.lnc_RNA ⇒ Object

A non-coding RNA over 200nucleotides in length. (http://purl.obolibrary.org/obo/SO_0001877)

# File 'lib/biointerchange/so.rb', line 11467

def self.lnc_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001877')
end

.locus_control_region ⇒ Object

A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene. (http://purl.obolibrary.org/obo/SO_0000037)

# File 'lib/biointerchange/so.rb', line 531

def self.locus_control_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000037')
end

.long_terminal_repeat ⇒ Object

A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses. (http://purl.obolibrary.org/obo/SO_0000286)

# File 'lib/biointerchange/so.rb', line 2037

def self.long_terminal_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000286')
end

.loss_of_heterozygosity ⇒ Object

A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene. (http://purl.obolibrary.org/obo/SO_0001786)

# File 'lib/biointerchange/so.rb', line 10921

def self.loss_of_heterozygosity
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001786')
end

.lost ⇒ Object

X lost Y if X is a variant_of X' and Y part of X' but not X. (http://purl.obolibrary.org/obo/so_2_5_2.obo#lost)

# File 'lib/biointerchange/so.rb', line 167

def self.lost
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#lost')
end

.low_complexity ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001004)

# File 'lib/biointerchange/so.rb', line 6299

def self.low_complexity
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001004')
end

.low_complexity_region ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001005)

# File 'lib/biointerchange/so.rb', line 6305

def self.low_complexity_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001005')
end

.loxP_site ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000346)

# File 'lib/biointerchange/so.rb', line 2397

def self.loxP_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000346')
end

.LTR_component ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000848)

# File 'lib/biointerchange/so.rb', line 5369

def self.LTR_component
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000848')
end

.LTR_retrotransposon ⇒ Object

A retrotransposon flanked by long terminal repeat sequences. (http://purl.obolibrary.org/obo/SO_0000186)

# File 'lib/biointerchange/so.rb', line 1437

def self.LTR_retrotransposon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000186')
end

.lysidine ⇒ Object

Lysidine is a modified cytidine. (http://purl.obolibrary.org/obo/SO_0001289)

# File 'lib/biointerchange/so.rb', line 7999

def self.lysidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001289')
end

.lysine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001450)

# File 'lib/biointerchange/so.rb', line 8959

def self.lysine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001450')
end

.lysine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding lysyl tRNA (SO:0000265). (http://purl.obolibrary.org/obo/SO_0000222)

# File 'lib/biointerchange/so.rb', line 1653

def self.lysine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000222')
end

.lysosomal_localization_signal ⇒ Object

A polypeptide region that targets a polypeptide to the lysosome. (http://purl.obolibrary.org/obo/SO_0001530)

# File 'lib/biointerchange/so.rb', line 9439

def self.lysosomal_localization_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001530')
end

.lysyl_tRNA ⇒ Object

A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region. (http://purl.obolibrary.org/obo/SO_0000265)

# File 'lib/biointerchange/so.rb', line 1911

def self.lysyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000265')
end

.M26_binding_site ⇒ Object

A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components. (http://purl.obolibrary.org/obo/SO_0001900)

# File 'lib/biointerchange/so.rb', line 11605

def self.M26_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001900')
end

.macronuclear_chromosome ⇒ Object

A chromosome originating in a macronucleus. (http://purl.obolibrary.org/obo/SO_0000824)

# File 'lib/biointerchange/so.rb', line 5237

def self.macronuclear_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000824')
end

.macronuclear_sequence ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000083)

# File 'lib/biointerchange/so.rb', line 815

def self.macronuclear_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000083')
end

.macronucleus_destined_segment ⇒ Object

A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome. (http://purl.obolibrary.org/obo/SO_0000672)

# File 'lib/biointerchange/so.rb', line 4355

def self.macronucleus_destined_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000672')
end

.major_TSS ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001238)

# File 'lib/biointerchange/so.rb', line 7699

def self.major_TSS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001238')
end

.mannosyl_queuosine ⇒ Object

Mannosyl_queuosine is a modified 7-deazoguanosine. (http://purl.obolibrary.org/obo/SO_0001320)

# File 'lib/biointerchange/so.rb', line 8185

def self.mannosyl_queuosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001320')
end

.match ⇒ Object

A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. (http://purl.obolibrary.org/obo/SO_0000343)

# File 'lib/biointerchange/so.rb', line 2379

def self.match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000343')
end

.match_part ⇒ Object

A part of a match, for example an hsp from blast is a match_part. (http://purl.obolibrary.org/obo/SO_0000039)

# File 'lib/biointerchange/so.rb', line 543

def self.match_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000039')
end

.match_set ⇒ Object

A collection of match parts. (http://purl.obolibrary.org/obo/SO_0000038)

# File 'lib/biointerchange/so.rb', line 537

def self.match_set
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000038')
end

.maternal_uniparental_disomy ⇒ Object

Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father. (http://purl.obolibrary.org/obo/SO_0001745)

# File 'lib/biointerchange/so.rb', line 10681

def self.maternal_uniparental_disomy
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001745')
end

.maternal_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001775)

# File 'lib/biointerchange/so.rb', line 10861

def self.maternal_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001775')
end

.maternally_imprinted ⇒ Object

The maternal copy of the gene is modified, rendering it transcriptionally silent. (http://purl.obolibrary.org/obo/SO_0000135)

# File 'lib/biointerchange/so.rb', line 1127

def self.maternally_imprinted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000135')
end

.maternally_imprinted_gene ⇒ Object

A gene that is maternally_imprinted. (http://purl.obolibrary.org/obo/SO_0000888)

# File 'lib/biointerchange/so.rb', line 5609

def self.maternally_imprinted_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000888')
end

.mathematically_defined_repeat ⇒ Object

A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness. (http://purl.obolibrary.org/obo/SO_0001642)

# File 'lib/biointerchange/so.rb', line 10087

def self.mathematically_defined_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001642')
end

.mating_type_M_box ⇒ Object

A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc. (http://purl.obolibrary.org/obo/SO_0001852)

# File 'lib/biointerchange/so.rb', line 11317

def self.mating_type_M_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001852')
end

.mating_type_region ⇒ Object

A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type. (http://purl.obolibrary.org/obo/SO_0001789)

# File 'lib/biointerchange/so.rb', line 10939

def self.mating_type_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001789')
end

.mating_type_region_motif ⇒ Object

DNA motif that is a component of a mating type region. (http://purl.obolibrary.org/obo/SO_0001999)

# File 'lib/biointerchange/so.rb', line 12197

def self.mating_type_region_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001999')
end

.matrix_attachment_site ⇒ Object

A DNA region that is required for the binding of chromatin to the nuclear matrix. (http://purl.obolibrary.org/obo/SO_0000036)

# File 'lib/biointerchange/so.rb', line 525

def self.matrix_attachment_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000036')
end

.mature_miRNA_variant ⇒ Object

A transcript variant located with the sequence of the mature miRNA. (http://purl.obolibrary.org/obo/SO_0001620)

# File 'lib/biointerchange/so.rb', line 9961

def self.mature_miRNA_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001620')
end

.mature_protein_region ⇒ Object

The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide. (http://purl.obolibrary.org/obo/SO_0000419)

# File 'lib/biointerchange/so.rb', line 2829

def self.mature_protein_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000419')
end

.mature_transcript ⇒ Object

A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified. (http://purl.obolibrary.org/obo/SO_0000233)

# File 'lib/biointerchange/so.rb', line 1719

def self.mature_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000233')
end

.mature_transcript_region ⇒ Object

A region of a mature transcript. (http://purl.obolibrary.org/obo/SO_0000834)

# File 'lib/biointerchange/so.rb', line 5285

def self.mature_transcript_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000834')
end

.maxicircle ⇒ Object

A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method. (http://purl.obolibrary.org/obo/SO_0000742)

# File 'lib/biointerchange/so.rb', line 4775

def self.maxicircle
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000742')
end

.maxicircle_gene ⇒ Object

A mitochondrial gene located in a maxicircle. (http://purl.obolibrary.org/obo/SO_0000654)

# File 'lib/biointerchange/so.rb', line 4247

def self.maxicircle_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000654')
end

.maximally_overlaps ⇒ Object

A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y. (http://purl.obolibrary.org/obo/so_2_5_2.obo#maximally_overlaps)

# File 'lib/biointerchange/so.rb', line 173

def self.maximally_overlaps
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#maximally_overlaps')
end

.MCB ⇒ Object

A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle. (http://purl.obolibrary.org/obo/SO_0001855)

# File 'lib/biointerchange/so.rb', line 11335

def self.MCB
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001855')
end

.member_of ⇒ Object

A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444. (http://purl.obolibrary.org/obo/so_2_5_2.obo#member_of)

# File 'lib/biointerchange/so.rb', line 179

def self.member_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#member_of')
end

.member_of_regulon ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_1001217)

# File 'lib/biointerchange/so.rb', line 13451

def self.member_of_regulon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001217')
end

.membrane_peptide_loop ⇒ Object

Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane. (http://purl.obolibrary.org/obo/SO_0001076)

# File 'lib/biointerchange/so.rb', line 6727

def self.membrane_peptide_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001076')
end

.membrane_structure ⇒ Object

Arrangement of the polypeptide with respect to the lipid bilayer. (http://purl.obolibrary.org/obo/SO_0001071)

# File 'lib/biointerchange/so.rb', line 6697

def self.membrane_structure
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001071')
end

.metabolic_island ⇒ Object

A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria. (http://purl.obolibrary.org/obo/SO_0000774)

# File 'lib/biointerchange/so.rb', line 4961

def self.metabolic_island
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000774')
end

.metal_binding_site ⇒ Object

A binding site that, in the molecule, interacts selectively and non-covalently with metal ions. (http://purl.obolibrary.org/obo/SO_0001656)

# File 'lib/biointerchange/so.rb', line 10147

def self.metal_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001656')
end

.methionine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001442)

# File 'lib/biointerchange/so.rb', line 8911

def self.methionine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001442')
end

.methionine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding methionyl tRNA (SO:0000266). (http://purl.obolibrary.org/obo/SO_0000223)

# File 'lib/biointerchange/so.rb', line 1659

def self.methionine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000223')
end

.methionyl_tRNA ⇒ Object

A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region. (http://purl.obolibrary.org/obo/SO_0000266)

# File 'lib/biointerchange/so.rb', line 1917

def self.methionyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000266')
end

.methylated_adenine ⇒ Object

A modified base in which adenine has been methylated. (http://purl.obolibrary.org/obo/SO_0000161)

# File 'lib/biointerchange/so.rb', line 1283

def self.methylated_adenine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000161')
end

.methylated_cytosine ⇒ Object

A methylated deoxy-cytosine. (http://purl.obolibrary.org/obo/SO_0000114)

# File 'lib/biointerchange/so.rb', line 1001

def self.methylated_cytosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000114')
end

.methylated_DNA_base_feature ⇒ Object

A nucleotide modified by methylation. (http://purl.obolibrary.org/obo/SO_0000306)

# File 'lib/biointerchange/so.rb', line 2157

def self.methylated_DNA_base_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000306')
end

.methylation_guide_snoRNA ⇒ Object

A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue. (http://purl.obolibrary.org/obo/SO_0005841)

# File 'lib/biointerchange/so.rb', line 12263

def self.methylation_guide_snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005841')
end

.methylation_guide_snoRNA_primary_transcript ⇒ Object

A primary transcript encoding a methylation guide small nucleolar RNA. (http://purl.obolibrary.org/obo/SO_0000580)

# File 'lib/biointerchange/so.rb', line 3803

def self.methylation_guide_snoRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000580')
end

.methylinosine ⇒ Object

A modified RNA base in which methylhypoxanthine is bound to the ribose ring. (http://purl.obolibrary.org/obo/SO_0001233)

# File 'lib/biointerchange/so.rb', line 7669

def self.methylinosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001233')
end

.methylwyosine ⇒ Object

Methylwyosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001337)

# File 'lib/biointerchange/so.rb', line 8287

def self.methylwyosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001337')
end

.MicF_RNA ⇒ Object

A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message. (http://purl.obolibrary.org/obo/SO_0000383)

# File 'lib/biointerchange/so.rb', line 2613

def self.MicF_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000383')
end

.microarray_oligo ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000328)

# File 'lib/biointerchange/so.rb', line 2289

def self.microarray_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000328')
end

.micronuclear_chromosome ⇒ Object

A chromosome originating in a micronucleus. (http://purl.obolibrary.org/obo/SO_0000825)

# File 'lib/biointerchange/so.rb', line 5243

def self.micronuclear_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000825')
end

.micronuclear_sequence ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000084)

# File 'lib/biointerchange/so.rb', line 821

def self.micronuclear_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000084')
end

.microsatellite ⇒ Object

A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem. (http://purl.obolibrary.org/obo/SO_0000289)

# File 'lib/biointerchange/so.rb', line 2055

def self.microsatellite
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000289')
end

.mini_exon_donor_RNA ⇒ Object

A primary transcript that donates the spliced leader to other mRNA. (http://purl.obolibrary.org/obo/SO_0000635)

# File 'lib/biointerchange/so.rb', line 4133

def self.mini_exon_donor_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000635')
end

.mini_gene ⇒ Object

By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA. (http://purl.obolibrary.org/obo/SO_0000815)

# File 'lib/biointerchange/so.rb', line 5183

def self.mini_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000815')
end

.minicircle ⇒ Object

A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs. (http://purl.obolibrary.org/obo/SO_0000980)

# File 'lib/biointerchange/so.rb', line 6155

def self.minicircle
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000980')
end

.minicircle_gene ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000975)

# File 'lib/biointerchange/so.rb', line 6125

def self.minicircle_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000975')
end

.minisatellite ⇒ Object

A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp. (http://purl.obolibrary.org/obo/SO_0000643)

# File 'lib/biointerchange/so.rb', line 4181

def self.minisatellite
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000643')
end

.minor_TSS ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001239)

# File 'lib/biointerchange/so.rb', line 7705

def self.minor_TSS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001239')
end

.minus_10_signal ⇒ Object

A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70. (http://purl.obolibrary.org/obo/SO_0000175)

# File 'lib/biointerchange/so.rb', line 1367

def self.minus_10_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000175')
end

.minus_12_signal ⇒ Object

A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54. (http://purl.obolibrary.org/obo/SO_0001673)

# File 'lib/biointerchange/so.rb', line 10249

def self.minus_12_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001673')
end

.minus_1_frameshift ⇒ Object

A frameshift caused by deleting one base. (http://purl.obolibrary.org/obo/SO_0000866)

# File 'lib/biointerchange/so.rb', line 5477

def self.minus_1_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000866')
end

.minus_1_frameshift_variant ⇒ Object

A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead. (http://purl.obolibrary.org/obo/SO_0001592)

# File 'lib/biointerchange/so.rb', line 9793

def self.minus_1_frameshift_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001592')
end

.minus_1_translationally_frameshifted ⇒ Object

An attribute describing a translational frameshift of -1. (http://purl.obolibrary.org/obo/SO_1001262)

# File 'lib/biointerchange/so.rb', line 13517

def self.minus_1_translationally_frameshifted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001262')
end

.minus_24_signal ⇒ Object

A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54. (http://purl.obolibrary.org/obo/SO_0001674)

# File 'lib/biointerchange/so.rb', line 10255

def self.minus_24_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001674')
end

.minus_2_frameshift ⇒ Object

A frameshift caused by deleting two bases. (http://purl.obolibrary.org/obo/SO_0000867)

# File 'lib/biointerchange/so.rb', line 5483

def self.minus_2_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000867')
end

.minus_2_frameshift_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001593)

# File 'lib/biointerchange/so.rb', line 9799

def self.minus_2_frameshift_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001593')
end

.minus_35_signal ⇒ Object

A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70. (http://purl.obolibrary.org/obo/SO_0000176)

# File 'lib/biointerchange/so.rb', line 1373

def self.minus_35_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000176')
end

.miRNA ⇒ Object

Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. (http://purl.obolibrary.org/obo/SO_0000276)

# File 'lib/biointerchange/so.rb', line 1977

def self.miRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000276')
end

.miRNA_antiguide ⇒ Object

A region of the pri miRNA that basepairs with the guide to form the hairpin. (http://purl.obolibrary.org/obo/SO_0001473)

# File 'lib/biointerchange/so.rb', line 9097

def self.miRNA_antiguide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001473')
end

.miRNA_encoding ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000571)

# File 'lib/biointerchange/so.rb', line 3749

def self.miRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000571')
end

.miRNA_gene ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001265)

# File 'lib/biointerchange/so.rb', line 7855

def self.miRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001265')
end

.miRNA_loop ⇒ Object

The loop of the hairpin loop formed by folding of the pre-miRNA. (http://purl.obolibrary.org/obo/SO_0001246)

# File 'lib/biointerchange/so.rb', line 7741

def self.miRNA_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001246')
end

.miRNA_primary_transcript ⇒ Object

A primary transcript encoding a micro RNA. (http://purl.obolibrary.org/obo/SO_0000647)

# File 'lib/biointerchange/so.rb', line 4205

def self.miRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000647')
end

.miRNA_primary_transcript_region ⇒ Object

A part of an miRNA primary_transcript. (http://purl.obolibrary.org/obo/SO_0001243)

# File 'lib/biointerchange/so.rb', line 7723

def self.miRNA_primary_transcript_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001243')
end

.miRNA_stem ⇒ Object

The stem of the hairpin loop formed by folding of the pre-miRNA. (http://purl.obolibrary.org/obo/SO_0001245)

# File 'lib/biointerchange/so.rb', line 7735

def self.miRNA_stem
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001245')
end

.miRNA_target_site ⇒ Object

A miRNA target site is a binding site where the molecule is a micro RNA. (http://purl.obolibrary.org/obo/SO_0000934)

# File 'lib/biointerchange/so.rb', line 5885

def self.miRNA_target_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000934')
end

.mirtron ⇒ Object

A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage. (http://purl.obolibrary.org/obo/SO_0001034)

# File 'lib/biointerchange/so.rb', line 6479

def self.mirtron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001034')
end

.missense_variant ⇒ Object

A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved. (http://purl.obolibrary.org/obo/SO_0001583)

# File 'lib/biointerchange/so.rb', line 9751

def self.missense_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001583')
end

.MITE ⇒ Object

A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins. (http://purl.obolibrary.org/obo/SO_0000338)

# File 'lib/biointerchange/so.rb', line 2349

def self.MITE
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000338')
end

.mitochondrial_chromosome ⇒ Object

A chromosome originating in a mitochondria. (http://purl.obolibrary.org/obo/SO_0000819)

# File 'lib/biointerchange/so.rb', line 5207

def self.mitochondrial_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000819')
end

.mitochondrial_contig ⇒ Object

A contig of mitochondria derived sequences. (http://purl.obolibrary.org/obo/SO_0001921)

# File 'lib/biointerchange/so.rb', line 11731

def self.mitochondrial_contig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001921')
end

.mitochondrial_DNA ⇒ Object

This terms is used by MO. (http://purl.obolibrary.org/obo/SO_0001032)

# File 'lib/biointerchange/so.rb', line 6467

def self.mitochondrial_DNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001032')
end

.mitochondrial_DNA_read ⇒ Object

A sequencer read of a mitochondrial DNA sample. (http://purl.obolibrary.org/obo/SO_0001929)

# File 'lib/biointerchange/so.rb', line 11779

def self.mitochondrial_DNA_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001929')
end

.mitochondrial_sequence ⇒ Object

This term is mapped to MGED. Do not obsolete without consulting MGED ontology. (http://purl.obolibrary.org/obo/SO_0000737)

# File 'lib/biointerchange/so.rb', line 4745

def self.mitochondrial_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000737')
end

.mitochondrial_supercontig ⇒ Object

A scaffold composed of mitochondrial contigs. (http://purl.obolibrary.org/obo/SO_0001922)

# File 'lib/biointerchange/so.rb', line 11737

def self.mitochondrial_supercontig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001922')
end

.mitochondrial_targeting_signal ⇒ Object

A polypeptide region that targets a polypeptide to the mitochondrion. (http://purl.obolibrary.org/obo/SO_0001808)

# File 'lib/biointerchange/so.rb', line 11053

def self.mitochondrial_targeting_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001808')
end

.MNP ⇒ Object

A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT. (http://purl.obolibrary.org/obo/SO_0001013)

# File 'lib/biointerchange/so.rb', line 6353

def self.MNP
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001013')
end

.MNV ⇒ Object

A multiple nucleotide substitution in which the inserted sequence is the same length as the replaced sequence. (http://purl.obolibrary.org/obo/SO_0002007)

# File 'lib/biointerchange/so.rb', line 12245

def self.MNV
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002007')
end

.mobile ⇒ Object

An attribute describing a feature that has either intra-genome or intracellular mobility. (http://purl.obolibrary.org/obo/SO_0001234)

# File 'lib/biointerchange/so.rb', line 7675

def self.mobile
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001234')
end

.mobile_element_insertion ⇒ Object

A kind of insertion where the inserted sequence is a mobile element. (http://purl.obolibrary.org/obo/SO_0001837)

# File 'lib/biointerchange/so.rb', line 11227

def self.mobile_element_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001837')
end

.mobile_genetic_element ⇒ Object

A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome. (http://purl.obolibrary.org/obo/SO_0001037)

# File 'lib/biointerchange/so.rb', line 6497

def self.mobile_genetic_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001037')
end

.mobile_intron ⇒ Object

An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility. (http://purl.obolibrary.org/obo/SO_0000666)

# File 'lib/biointerchange/so.rb', line 4319

def self.mobile_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000666')
end

.modified_adenine ⇒ Object

A modified adenine DNA base feature. (http://purl.obolibrary.org/obo/SO_0001962)

# File 'lib/biointerchange/so.rb', line 11981

def self.modified_adenine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001962')
end

.modified_adenosine ⇒ Object

A modified adenine is an adenine base feature that has been altered. (http://purl.obolibrary.org/obo/SO_0001273)

# File 'lib/biointerchange/so.rb', line 7903

def self.modified_adenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001273')
end

.modified_amino_acid_feature ⇒ Object

A post translationally modified amino acid feature. (http://purl.obolibrary.org/obo/SO_0001385)

# File 'lib/biointerchange/so.rb', line 8575

def self.modified_amino_acid_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001385')
end

.modified_cytidine ⇒ Object

A modified cytidine is a cytidine base feature which has been altered. (http://purl.obolibrary.org/obo/SO_0001275)

# File 'lib/biointerchange/so.rb', line 7915

def self.modified_cytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001275')
end

.modified_cytosine ⇒ Object

A modified cytosine DNA base feature. (http://purl.obolibrary.org/obo/SO_0001963)

# File 'lib/biointerchange/so.rb', line 11987

def self.modified_cytosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001963')
end

.modified_DNA_base ⇒ Object

A modified nucleotide, i.e. a nucleotide other than A, T, C. G. (http://purl.obolibrary.org/obo/SO_0000305)

# File 'lib/biointerchange/so.rb', line 2151

def self.modified_DNA_base
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000305')
end

.modified_glycine ⇒ Object

A post translationally modified glycine amino acid feature. (http://purl.obolibrary.org/obo/SO_0001386)

# File 'lib/biointerchange/so.rb', line 8581

def self.modified_glycine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001386')
end

.modified_guanine ⇒ Object

A modified guanine DNA base feature. (http://purl.obolibrary.org/obo/SO_0001964)

# File 'lib/biointerchange/so.rb', line 11993

def self.modified_guanine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001964')
end

.modified_guanosine ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001276)

# File 'lib/biointerchange/so.rb', line 7921

def self.modified_guanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001276')
end

.modified_inosine ⇒ Object

A modified inosine is an inosine base feature that has been altered. (http://purl.obolibrary.org/obo/SO_0001274)

# File 'lib/biointerchange/so.rb', line 7909

def self.modified_inosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001274')
end

.modified_L_alanine ⇒ Object

A post translationally modified alanine amino acid feature. (http://purl.obolibrary.org/obo/SO_0001387)

# File 'lib/biointerchange/so.rb', line 8587

def self.modified_L_alanine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001387')
end

.modified_L_arginine ⇒ Object

A post translationally modified arginine amino acid feature. (http://purl.obolibrary.org/obo/SO_0001406)

# File 'lib/biointerchange/so.rb', line 8701

def self.modified_L_arginine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001406')
end

.modified_L_asparagine ⇒ Object

A post translationally modified asparagine amino acid feature. (http://purl.obolibrary.org/obo/SO_0001388)

# File 'lib/biointerchange/so.rb', line 8593

def self.modified_L_asparagine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001388')
end

.modified_L_aspartic_acid ⇒ Object

A post translationally modified aspartic acid amino acid feature. (http://purl.obolibrary.org/obo/SO_0001389)

# File 'lib/biointerchange/so.rb', line 8599

def self.modified_L_aspartic_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001389')
end

.modified_L_cysteine ⇒ Object

A post translationally modified cysteine amino acid feature. (http://purl.obolibrary.org/obo/SO_0001390)

# File 'lib/biointerchange/so.rb', line 8605

def self.modified_L_cysteine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001390')
end

.modified_L_glutamic_acid ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001391)

# File 'lib/biointerchange/so.rb', line 8611

def self.modified_L_glutamic_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001391')
end

.modified_L_glutamine ⇒ Object

A post translationally modified glutamine amino acid feature. (http://purl.obolibrary.org/obo/SO_0001394)

# File 'lib/biointerchange/so.rb', line 8629

def self.modified_L_glutamine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001394')
end

.modified_L_histidine ⇒ Object

A post translationally modified histidie amino acid feature. (http://purl.obolibrary.org/obo/SO_0001398)

# File 'lib/biointerchange/so.rb', line 8653

def self.modified_L_histidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001398')
end

.modified_L_isoleucine ⇒ Object

A post translationally modified isoleucine amino acid feature. (http://purl.obolibrary.org/obo/SO_0001396)

# File 'lib/biointerchange/so.rb', line 8641

def self.modified_L_isoleucine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001396')
end

.modified_L_leucine ⇒ Object

A post translationally modified leucine amino acid feature. (http://purl.obolibrary.org/obo/SO_0001401)

# File 'lib/biointerchange/so.rb', line 8671

def self.modified_L_leucine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001401')
end

.modified_L_lysine ⇒ Object

A post translationally modified lysine amino acid feature. (http://purl.obolibrary.org/obo/SO_0001400)

# File 'lib/biointerchange/so.rb', line 8665

def self.modified_L_lysine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001400')
end

.modified_L_methionine ⇒ Object

A post translationally modified methionine amino acid feature. (http://purl.obolibrary.org/obo/SO_0001395)

# File 'lib/biointerchange/so.rb', line 8635

def self.modified_L_methionine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001395')
end

.modified_L_phenylalanine ⇒ Object

A post translationally modified phenylalanine amino acid feature. (http://purl.obolibrary.org/obo/SO_0001397)

# File 'lib/biointerchange/so.rb', line 8647

def self.modified_L_phenylalanine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001397')
end

.modified_L_proline ⇒ Object

A post translationally modified proline amino acid feature. (http://purl.obolibrary.org/obo/SO_0001404)

# File 'lib/biointerchange/so.rb', line 8689

def self.modified_L_proline
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001404')
end

.modified_L_selenocysteine ⇒ Object

A post translationally modified selenocysteine amino acid feature. (http://purl.obolibrary.org/obo/SO_0001402)

# File 'lib/biointerchange/so.rb', line 8677

def self.modified_L_selenocysteine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001402')
end

.modified_L_serine ⇒ Object

A post translationally modified serine amino acid feature. (http://purl.obolibrary.org/obo/SO_0001399)

# File 'lib/biointerchange/so.rb', line 8659

def self.modified_L_serine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001399')
end

.modified_L_threonine ⇒ Object

A post translationally modified threonine amino acid feature. (http://purl.obolibrary.org/obo/SO_0001392)

# File 'lib/biointerchange/so.rb', line 8617

def self.modified_L_threonine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001392')
end

.modified_L_tryptophan ⇒ Object

A post translationally modified tryptophan amino acid feature. (http://purl.obolibrary.org/obo/SO_0001393)

# File 'lib/biointerchange/so.rb', line 8623

def self.modified_L_tryptophan
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001393')
end

.modified_L_tyrosine ⇒ Object

A post translationally modified tyrosine amino acid feature. (http://purl.obolibrary.org/obo/SO_0001405)

# File 'lib/biointerchange/so.rb', line 8695

def self.modified_L_tyrosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001405')
end

.modified_L_valine ⇒ Object

A post translationally modified valine amino acid feature. (http://purl.obolibrary.org/obo/SO_0001403)

# File 'lib/biointerchange/so.rb', line 8683

def self.modified_L_valine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001403')
end

.modified_RNA_base_feature ⇒ Object

A post_transcriptionally modified base. (http://purl.obolibrary.org/obo/SO_0000250)

# File 'lib/biointerchange/so.rb', line 1821

def self.modified_RNA_base_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000250')
end

.modified_uridine ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001277)

# File 'lib/biointerchange/so.rb', line 7927

def self.modified_uridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001277')
end

.molecular_contact_region ⇒ Object

A region that is involved a contact with another molecule. (http://purl.obolibrary.org/obo/SO_0100002)

# File 'lib/biointerchange/so.rb', line 12359

def self.molecular_contact_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100002')
end

.monocistronic ⇒ Object

An attribute describing a sequence that contains the code for one gene product. (http://purl.obolibrary.org/obo/SO_0000878)

# File 'lib/biointerchange/so.rb', line 5549

def self.monocistronic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000878')
end

.monocistronic_mRNA ⇒ Object

An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap. (http://purl.obolibrary.org/obo/SO_0000633)

# File 'lib/biointerchange/so.rb', line 4121

def self.monocistronic_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000633')
end

.monocistronic_primary_transcript ⇒ Object

A primary transcript encoding for one gene product. (http://purl.obolibrary.org/obo/SO_0000632)

# File 'lib/biointerchange/so.rb', line 4115

def self.monocistronic_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000632')
end

.monocistronic_transcript ⇒ Object

A transcript that is monocistronic. (http://purl.obolibrary.org/obo/SO_0000665)

# File 'lib/biointerchange/so.rb', line 4313

def self.monocistronic_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000665')
end

.monomeric_repeat ⇒ Object

A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem. (http://purl.obolibrary.org/obo/SO_0001934)

# File 'lib/biointerchange/so.rb', line 11809

def self.monomeric_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001934')
end

.morpholino_backbone ⇒ Object

An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages. (http://purl.obolibrary.org/obo/SO_0001183)

# File 'lib/biointerchange/so.rb', line 7369

def self.morpholino_backbone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001183')
end

.morpholino_oligo ⇒ Object

Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino. (http://purl.obolibrary.org/obo/SO_0000034)

# File 'lib/biointerchange/so.rb', line 513

def self.morpholino_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000034')
end

.mRNA ⇒ Object

Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. (http://purl.obolibrary.org/obo/SO_0000234)

# File 'lib/biointerchange/so.rb', line 1725

def self.mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000234')
end

.mRNA_attribute ⇒ Object

An attribute describing an mRNA feature. (http://purl.obolibrary.org/obo/SO_0000863)

# File 'lib/biointerchange/so.rb', line 5459

def self.mRNA_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000863')
end

.mRNA_by_polyadenylation_status ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000245)

# File 'lib/biointerchange/so.rb', line 1791

def self.mRNA_by_polyadenylation_status
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000245')
end

.mRNA_contig ⇒ Object

A contig composed of mRNA_reads. (http://purl.obolibrary.org/obo/SO_0001829)

# File 'lib/biointerchange/so.rb', line 11179

def self.mRNA_contig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001829')
end

.mRNA_not_polyadenylated ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000247)

# File 'lib/biointerchange/so.rb', line 1803

def self.mRNA_not_polyadenylated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000247')
end

.mRNA_read ⇒ Object

A sequencer read of an mRNA substrate. (http://purl.obolibrary.org/obo/SO_0001827)

# File 'lib/biointerchange/so.rb', line 11167

def self.mRNA_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001827')
end

.mRNA_recoded_by_codon_redefinition ⇒ Object

A recoded_mRNA that was modified by an alteration of codon meaning. (http://purl.obolibrary.org/obo/SO_1001265)

# File 'lib/biointerchange/so.rb', line 13535

def self.mRNA_recoded_by_codon_redefinition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001265')
end

.mRNA_recoded_by_translational_bypass ⇒ Object

A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon. (http://purl.obolibrary.org/obo/SO_1001264)

# File 'lib/biointerchange/so.rb', line 13529

def self.mRNA_recoded_by_translational_bypass
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001264')
end

.mRNA_region ⇒ Object

A region of an mRNA. (http://purl.obolibrary.org/obo/SO_0000836)

# File 'lib/biointerchange/so.rb', line 5297

def self.mRNA_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000836')
end

.mRNA_with_frameshift ⇒ Object

An mRNA with a frameshift. (http://purl.obolibrary.org/obo/SO_0000108)

# File 'lib/biointerchange/so.rb', line 965

def self.mRNA_with_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000108')
end

.mRNA_with_minus_1_frameshift ⇒ Object

An mRNA with a minus 1 frameshift. (http://purl.obolibrary.org/obo/SO_0000282)

# File 'lib/biointerchange/so.rb', line 2013

def self.mRNA_with_minus_1_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000282')
end

.mRNA_with_minus_2_frameshift ⇒ Object

A mRNA with a minus 2 frameshift. (http://purl.obolibrary.org/obo/SO_0000335)

# File 'lib/biointerchange/so.rb', line 2331

def self.mRNA_with_minus_2_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000335')
end

.mRNA_with_plus_1_frameshift ⇒ Object

An mRNA with a plus 1 frameshift. (http://purl.obolibrary.org/obo/SO_0000321)

# File 'lib/biointerchange/so.rb', line 2247

def self.mRNA_with_plus_1_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000321')
end

.mRNA_with_plus_2_frameshift ⇒ Object

An mRNA with a plus 2 frameshift. (http://purl.obolibrary.org/obo/SO_0000329)

# File 'lib/biointerchange/so.rb', line 2295

def self.mRNA_with_plus_2_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000329')
end

.mt_gene ⇒ Object

A gene located in mitochondrial sequence. (http://purl.obolibrary.org/obo/SO_0000088)

# File 'lib/biointerchange/so.rb', line 845

def self.mt_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000088')
end

.MTE ⇒ Object

A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159). (http://purl.obolibrary.org/obo/SO_0001162)

# File 'lib/biointerchange/so.rb', line 7243

def self.MTE
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001162')
end

.mutated_variant_site ⇒ Object

Site which has been experimentally altered. (http://purl.obolibrary.org/obo/SO_0001148)

# File 'lib/biointerchange/so.rb', line 7159

def self.mutated_variant_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001148')
end

.mutation_causing_inframe_polypeptide_N_terminal_elongation ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000106)

# File 'lib/biointerchange/so.rb', line 13031

def self.mutation_causing_inframe_polypeptide_N_terminal_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000106')
end

.mutation_causing_out_of_frame_polypeptide_C_terminal_elongation ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000109)

# File 'lib/biointerchange/so.rb', line 13049

def self.mutation_causing_out_of_frame_polypeptide_C_terminal_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000109')
end

.mutation_causing_out_of_frame_polypeptide_N_terminal_elongation ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000107)

# File 'lib/biointerchange/so.rb', line 13037

def self.mutation_causing_out_of_frame_polypeptide_N_terminal_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000107')
end

.mutation_causing_polypeptide_C_terminal_elongation ⇒ Object

. (http://purl.obolibrary.org/obo/SO_1000101)

# File 'lib/biointerchange/so.rb', line 13001

def self.mutation_causing_polypeptide_C_terminal_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000101')
end

.mutation_causing_polypeptide_N_terminal_elongation ⇒ Object

. (http://purl.obolibrary.org/obo/SO_1000100)

# File 'lib/biointerchange/so.rb', line 12995

def self.mutation_causing_polypeptide_N_terminal_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000100')
end

.mutaton_causing_inframe_polypeptide_C_terminal_elongation ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_1000108)

# File 'lib/biointerchange/so.rb', line 13043

def self.mutaton_causing_inframe_polypeptide_C_terminal_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000108')
end

.N2_2_prime_O_dimethylguanosine ⇒ Object

N2_2prime_O_dimethylguanosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001329)

# File 'lib/biointerchange/so.rb', line 8239

def self.N2_2_prime_O_dimethylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001329')
end

.N2_7_2prirme_O_trimethylguanosine ⇒ Object

N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001343)

# File 'lib/biointerchange/so.rb', line 8323

def self.N2_7_2prirme_O_trimethylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001343')
end

.N2_7_dimethylguanosine ⇒ Object

N2_7_dimethylguanosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001338)

# File 'lib/biointerchange/so.rb', line 8293

def self.N2_7_dimethylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001338')
end

.N2_methylguanosine ⇒ Object

N2_methylguanosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001325)

# File 'lib/biointerchange/so.rb', line 8215

def self.N2_methylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001325')
end

.N2_N2_2_prime_O_trimethylguanosine ⇒ Object

N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001330)

# File 'lib/biointerchange/so.rb', line 8245

def self.N2_N2_2_prime_O_trimethylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001330')
end

.N2_N2_7_trimethylguanosine ⇒ Object

N2_N2_7_trimethylguanosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001339)

# File 'lib/biointerchange/so.rb', line 8299

def self.N2_N2_7_trimethylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001339')
end

.N2_N2_dimethylguanosine ⇒ Object

N2_N2_dimethylguanosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001328)

# File 'lib/biointerchange/so.rb', line 8233

def self.N2_N2_dimethylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001328')
end

.N4_2_prime_O_dimethylcytidine ⇒ Object

N4,2'-O-dimethylcytidine is a modified cytidine. (http://purl.obolibrary.org/obo/SO_0001291)

# File 'lib/biointerchange/so.rb', line 8011

def self.N4_2_prime_O_dimethylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001291')
end

.N4_acetyl_2_prime_O_methylcytidine ⇒ Object

N4-acetyl-2'-O-methylcytidine is a modified cytidine. (http://purl.obolibrary.org/obo/SO_0001288)

# File 'lib/biointerchange/so.rb', line 7993

def self.N4_acetyl_2_prime_O_methylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001288')
end

.N4_acetylcytidine ⇒ Object

N4-acetylcytidine is a modified cytidine. (http://purl.obolibrary.org/obo/SO_0001285)

# File 'lib/biointerchange/so.rb', line 7975

def self.N4_acetylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001285')
end

.N4_methylcytidine ⇒ Object

N4-methylcytidine is a modified cytidine. (http://purl.obolibrary.org/obo/SO_0001290)

# File 'lib/biointerchange/so.rb', line 8005

def self.N4_methylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001290')
end

.N4_N4_2_prime_O_trimethylcytidine ⇒ Object

N4_N4_2_prime_O_trimethylcytidine is a modified cytidine. (http://purl.obolibrary.org/obo/SO_0001294)

# File 'lib/biointerchange/so.rb', line 8029

def self.N4_N4_2_prime_O_trimethylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001294')
end

.N6_2_prime_O_dimethyladenosine ⇒ Object

N6_2prime_O_dimethyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001312)

# File 'lib/biointerchange/so.rb', line 8137

def self.N6_2_prime_O_dimethyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001312')
end

.N6_acetyladenosine ⇒ Object

N6_acetyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001315)

# File 'lib/biointerchange/so.rb', line 8155

def self.N6_acetyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001315')
end

.N6_cis_hydroxyisopentenyl_adenosine ⇒ Object

N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001302)

# File 'lib/biointerchange/so.rb', line 8077

def self.N6_cis_hydroxyisopentenyl_adenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001302')
end

.N6_glycinylcarbamoyladenosine ⇒ Object

N6_glycinylcarbamoyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001304)

# File 'lib/biointerchange/so.rb', line 8089

def self.N6_glycinylcarbamoyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001304')
end

.N6_hydroxynorvalylcarbamoyladenosine ⇒ Object

N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001308)

# File 'lib/biointerchange/so.rb', line 8113

def self.N6_hydroxynorvalylcarbamoyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001308')
end

.N6_isopentenyladenosine ⇒ Object

N6_isopentenyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001300)

# File 'lib/biointerchange/so.rb', line 8065

def self.N6_isopentenyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001300')
end

.N6_methyl_N6_threonylcarbamoyladenosine ⇒ Object

N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001307)

# File 'lib/biointerchange/so.rb', line 8107

def self.N6_methyl_N6_threonylcarbamoyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001307')
end

.N6_methyladenine ⇒ Object

An adenine methylated at the 6 nitrogen. (http://purl.obolibrary.org/obo/SO_0001920)

# File 'lib/biointerchange/so.rb', line 11725

def self.N6_methyladenine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001920')
end

.N6_methyladenosine ⇒ Object

N6_methyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001297)

# File 'lib/biointerchange/so.rb', line 8047

def self.N6_methyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001297')
end

.N6_N6_2_prime_O_trimethyladenosine ⇒ Object

N6_N6_2prime_O_trimethyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001313)

# File 'lib/biointerchange/so.rb', line 8143

def self.N6_N6_2_prime_O_trimethyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001313')
end

.N6_N6_dimethyladenosine ⇒ Object

N6_N6_dimethyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001311)

# File 'lib/biointerchange/so.rb', line 8131

def self.N6_N6_dimethyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001311')
end

.N6_threonylcarbamoyladenosine ⇒ Object

N6_threonylcarbamoyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001305)

# File 'lib/biointerchange/so.rb', line 8095

def self.N6_threonylcarbamoyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001305')
end

.N_region ⇒ Object

Extra nucleotides inserted between rearranged immunoglobulin segments. (http://purl.obolibrary.org/obo/SO_0001835)

# File 'lib/biointerchange/so.rb', line 11215

def self.N_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001835')
end

.n_terminal_region ⇒ Object

The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa). (http://purl.obolibrary.org/obo/SO_0100014)

# File 'lib/biointerchange/so.rb', line 12431

def self.n_terminal_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100014')
end

.natural ⇒ Object

An attribute describing a feature that occurs in nature. (http://purl.obolibrary.org/obo/SO_0000782)

# File 'lib/biointerchange/so.rb', line 5009

def self.natural
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000782')
end

.natural_plasmid ⇒ Object

A plasmid that occurs naturally. (http://purl.obolibrary.org/obo/SO_0001476)

# File 'lib/biointerchange/so.rb', line 9115

def self.natural_plasmid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001476')
end

.natural_transposable_element ⇒ Object

TE that exists (or existed) in nature. (http://purl.obolibrary.org/obo/SO_0000797)

# File 'lib/biointerchange/so.rb', line 5099

def self.natural_transposable_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000797')
end

.natural_variant_site ⇒ Object

Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars. (http://purl.obolibrary.org/obo/SO_0001147)

# File 'lib/biointerchange/so.rb', line 7153

def self.natural_variant_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001147')
end

.nc_conserved_region ⇒ Object

Non-coding region of sequence similarity by descent from a common ancestor. (http://purl.obolibrary.org/obo/SO_0000334)

# File 'lib/biointerchange/so.rb', line 2325

def self.nc_conserved_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000334')
end

.nc_primary_transcript ⇒ Object

A primary transcript that is never translated into a protein. (http://purl.obolibrary.org/obo/SO_0000483)

# File 'lib/biointerchange/so.rb', line 3217

def self.nc_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000483')
end

.ncRNA ⇒ Object

An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product. (http://purl.obolibrary.org/obo/SO_0000655)

# File 'lib/biointerchange/so.rb', line 4253

def self.ncRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000655')
end

.ncRNA_gene ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001263)

# File 'lib/biointerchange/so.rb', line 7843

def self.ncRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001263')
end

.NDM2_motif ⇒ Object

A non directional promoter motif with consensus CGMYGYCR. (http://purl.obolibrary.org/obo/SO_0001167)

# File 'lib/biointerchange/so.rb', line 7273

def self.NDM2_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001167')
end

.NDM3_motif ⇒ Object

A non directional promoter motif with consensus sequence GAAAGCT. (http://purl.obolibrary.org/obo/SO_0001168)

# File 'lib/biointerchange/so.rb', line 7279

def self.NDM3_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001168')
end

.negative_sense_ssRNA_viral_sequence ⇒ Object

A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation. (http://purl.obolibrary.org/obo/SO_0001200)

# File 'lib/biointerchange/so.rb', line 7471

def self.negative_sense_ssRNA_viral_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001200')
end

.negatively_autoregulated ⇒ Object

The gene product is involved in its own transcriptional regulation where it decreases transcription. (http://purl.obolibrary.org/obo/SO_0000473)

# File 'lib/biointerchange/so.rb', line 3157

def self.negatively_autoregulated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000473')
end

.negatively_autoregulated_gene ⇒ Object

A gene that is negatively autoreguated. (http://purl.obolibrary.org/obo/SO_0000891)

# File 'lib/biointerchange/so.rb', line 5627

def self.negatively_autoregulated_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000891')
end

.nested_region ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001051)

# File 'lib/biointerchange/so.rb', line 6581

def self.nested_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001051')
end

.nested_repeat ⇒ Object

Either:

-- No comment or description provided. --
(http://purl.obolibrary.org/obo/SO_0001052)

Or:

A repeat that is disrupted by the insertion of another element.
(http://purl.obolibrary.org/obo/SO_0001649)

# File 'lib/biointerchange/so.rb', line 6591

def self.nested_repeat
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001052'), RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001649') ]
end

.nested_tandem_repeat ⇒ Object

An NTR is a nested repeat of two distinct tandem motifs interspersed with each other. (http://purl.obolibrary.org/obo/SO_0001658)

# File 'lib/biointerchange/so.rb', line 10159

def self.nested_tandem_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001658')
end

.nested_transposon ⇒ Object

Either:

-- No comment or description provided. --
(http://purl.obolibrary.org/obo/SO_0001053)

Or:

A transposon that is disrupted by the insertion of another element.
(http://purl.obolibrary.org/obo/SO_0001648)

# File 'lib/biointerchange/so.rb', line 6601

def self.nested_transposon
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001053'), RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001648') ]
end

.NMD_transcript_variant ⇒ Object

A variant in a transcript that is the target of NMD. (http://purl.obolibrary.org/obo/SO_0001621)

# File 'lib/biointerchange/so.rb', line 9967

def self.NMD_transcript_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001621')
end

.no_output ⇒ Object

An experimental region wherean analysis has been run and not produced any annotation. (http://purl.obolibrary.org/obo/SO_0100010)

# File 'lib/biointerchange/so.rb', line 12407

def self.no_output
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100010')
end

.non_adjacent_residues ⇒ Object

Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them. (http://purl.obolibrary.org/obo/SO_0001083)

# File 'lib/biointerchange/so.rb', line 6769

def self.non_adjacent_residues
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001083')
end

.non_canonical_five_prime_splice_site ⇒ Object

A 5' splice site which does not have the sequence "GT". (SO:ke) (http://purl.obolibrary.org/obo/SO_0000679)

# File 'lib/biointerchange/so.rb', line 4397

def self.non_canonical_five_prime_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000679')
end

.non_canonical_splice_site ⇒ Object

A splice site where the donor and acceptor sites differ from the canonical form. (http://purl.obolibrary.org/obo/SO_0000674)

# File 'lib/biointerchange/so.rb', line 4367

def self.non_canonical_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000674')
end

.non_canonical_start_codon ⇒ Object

A start codon that is not the usual AUG sequence. (http://purl.obolibrary.org/obo/SO_0000680)

# File 'lib/biointerchange/so.rb', line 4403

def self.non_canonical_start_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000680')
end

.non_canonical_three_prime_splice_site ⇒ Object

A 3' splice site that does not have the sequence "AG". (SO:ke) (http://purl.obolibrary.org/obo/SO_0000678)

# File 'lib/biointerchange/so.rb', line 4391

def self.non_canonical_three_prime_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000678')
end

.non_capped_primary_transcript ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000106)

# File 'lib/biointerchange/so.rb', line 953

def self.non_capped_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000106')
end

.non_coding_transcript_exon_variant ⇒ Object

A sequence variant that changes non-coding exon sequence in a non-coding transcript. (http://purl.obolibrary.org/obo/SO_0001792)

# File 'lib/biointerchange/so.rb', line 10957

def self.non_coding_transcript_exon_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001792')
end

.non_coding_transcript_intron_variant ⇒ Object

A transcript variant occurring within an intron of a non coding transcript. (http://purl.obolibrary.org/obo/SO_0001970)

# File 'lib/biointerchange/so.rb', line 12029

def self.non_coding_transcript_intron_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001970')
end

.non_coding_transcript_variant ⇒ Object

A transcript variant of a non coding RNA gene. (http://purl.obolibrary.org/obo/SO_0001619)

# File 'lib/biointerchange/so.rb', line 9955

def self.non_coding_transcript_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001619')
end

.non_conservative_amino_acid_substitution ⇒ Object

A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide. (http://purl.obolibrary.org/obo/SO_0001608)

# File 'lib/biointerchange/so.rb', line 9889

def self.non_conservative_amino_acid_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001608')
end

.non_conservative_missense_variant ⇒ Object

A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties. (http://purl.obolibrary.org/obo/SO_0001586)

# File 'lib/biointerchange/so.rb', line 9763

def self.non_conservative_missense_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001586')
end

.non_covalent_binding_site ⇒ Object

Binding site for any chemical group (co-enzyme, prosthetic group, etc.). (http://purl.obolibrary.org/obo/SO_0001091)

# File 'lib/biointerchange/so.rb', line 6817

def self.non_covalent_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001091')
end

.non_cytoplasmic_polypeptide_region ⇒ Object

Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm. (http://purl.obolibrary.org/obo/SO_0001074)

# File 'lib/biointerchange/so.rb', line 6715

def self.non_cytoplasmic_polypeptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001074')
end

.non_functional_homolog_of ⇒ Object

A relationship between a pseudogenic feature and its functional ancestor. (http://purl.obolibrary.org/obo/so_2_5_2.obo#non_functional_homolog_of)

# File 'lib/biointerchange/so.rb', line 185

def self.non_functional_homolog_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#non_functional_homolog_of')
end

.non_LTR_retrotransposon ⇒ Object

A retrotransposon without long terminal repeat sequences. (http://purl.obolibrary.org/obo/SO_0000189)

# File 'lib/biointerchange/so.rb', line 1455

def self.non_LTR_retrotransposon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000189')
end

.non_LTR_retrotransposon_polymeric_tract ⇒ Object

A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon. (http://purl.obolibrary.org/obo/SO_0000433)

# File 'lib/biointerchange/so.rb', line 2913

def self.non_LTR_retrotransposon_polymeric_tract
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000433')
end

.non_processed_pseudogene ⇒ Object

A pseudogene that arose from a means other than retrotransposition. (http://purl.obolibrary.org/obo/SO_0001760)

# File 'lib/biointerchange/so.rb', line 10771

def self.non_processed_pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001760')
end

.non_protein_coding ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000011)

# File 'lib/biointerchange/so.rb', line 381

def self.non_protein_coding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000011')
end

.non_synonymous ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001816)

# File 'lib/biointerchange/so.rb', line 11101

def self.non_synonymous
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001816')
end

.non_terminal_residue ⇒ Object

The residue at an extremity of the sequence is not the terminal residue. (http://purl.obolibrary.org/obo/SO_0001084)

# File 'lib/biointerchange/so.rb', line 6775

def self.non_terminal_residue
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001084')
end

.non_transcribed_region ⇒ Object

A region of the gene which is not transcribed. (http://purl.obolibrary.org/obo/SO_0000183)

# File 'lib/biointerchange/so.rb', line 1419

def self.non_transcribed_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000183')
end

.nonamer_of_recombination_feature_of_vertebrate_immune_system_gene ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000562)

# File 'lib/biointerchange/so.rb', line 3695

def self.nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000562')
end

.noncoding_exon ⇒ Object

An exon that does not contain any codons. (http://purl.obolibrary.org/obo/SO_0000198)

# File 'lib/biointerchange/so.rb', line 1509

def self.noncoding_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000198')
end

.noncoding_region_of_exon ⇒ Object

The maximal intersection of exon and UTR. (http://purl.obolibrary.org/obo/SO_0001214)

# File 'lib/biointerchange/so.rb', line 7555

def self.noncoding_region_of_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001214')
end

.noncontiguous_finished ⇒ Object

The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions. (http://purl.obolibrary.org/obo/SO_0001490)

# File 'lib/biointerchange/so.rb', line 9199

def self.noncontiguous_finished
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001490')
end

.nonsynonymous_variant ⇒ Object

A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change. (http://purl.obolibrary.org/obo/SO_0001992)

# File 'lib/biointerchange/so.rb', line 12155

def self.nonsynonymous_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001992')
end

.novel_sequence_insertion ⇒ Object

An insertion the sequence of which cannot be mapped to the reference genome. (http://purl.obolibrary.org/obo/SO_0001838)

# File 'lib/biointerchange/so.rb', line 11233

def self.novel_sequence_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001838')
end

.nuclear_chromosome ⇒ Object

A chromosome originating in a nucleus. (http://purl.obolibrary.org/obo/SO_0000828)

# File 'lib/biointerchange/so.rb', line 5249

def self.nuclear_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000828')
end

.nuclear_export_signal ⇒ Object

A polypeptide region that targets a polypeptide to he cytoplasm. (http://purl.obolibrary.org/obo/SO_0001531)

# File 'lib/biointerchange/so.rb', line 9445

def self.nuclear_export_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001531')
end

.nuclear_gene ⇒ Object

A gene from nuclear sequence. (http://purl.obolibrary.org/obo/SO_0000087)

# File 'lib/biointerchange/so.rb', line 839

def self.nuclear_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000087')
end

.nuclear_localization_signal ⇒ Object

A polypeptide region that targets a polypeptide to the nucleus. (http://purl.obolibrary.org/obo/SO_0001528)

# File 'lib/biointerchange/so.rb', line 9427

def self.nuclear_localization_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001528')
end

.nuclear_mitochondrial ⇒ Object

An attribute describing a nuclear pseudogene of a mitochndrial gene. (http://purl.obolibrary.org/obo/SO_0000899)

# File 'lib/biointerchange/so.rb', line 5675

def self.nuclear_mitochondrial
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000899')
end

.nuclear_mt_pseudogene ⇒ Object

A nuclear pseudogene of either coding or non-coding mitochondria derived sequence. (http://purl.obolibrary.org/obo/SO_0001044)

# File 'lib/biointerchange/so.rb', line 6539

def self.nuclear_mt_pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001044')
end

.nuclear_rim_localization_signal ⇒ Object

A polypeptide region that targets a polypeptide to the nuclear rim. (http://purl.obolibrary.org/obo/SO_0001534)

# File 'lib/biointerchange/so.rb', line 9463

def self.nuclear_rim_localization_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001534')
end

.nuclear_sequence ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000738)

# File 'lib/biointerchange/so.rb', line 4751

def self.nuclear_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000738')
end

.nuclease_binding_site ⇒ Object

A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease. (http://purl.obolibrary.org/obo/SO_0000059)

# File 'lib/biointerchange/so.rb', line 671

def self.nuclease_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000059')
end

.nuclease_hypersensitive_site ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000322)

# File 'lib/biointerchange/so.rb', line 2253

def self.nuclease_hypersensitive_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000322')
end

.nuclease_sensitive_site ⇒ Object

A region of nucleotide sequence targeted by a nuclease enzyme. (http://purl.obolibrary.org/obo/SO_0000684)

# File 'lib/biointerchange/so.rb', line 4427

def self.nuclease_sensitive_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000684')
end

.nucleic_acid ⇒ Object

An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. (http://purl.obolibrary.org/obo/SO_0000348)

# File 'lib/biointerchange/so.rb', line 2409

def self.nucleic_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000348')
end

.nucleomorph_gene ⇒ Object

A gene from nucleomorph sequence. (http://purl.obolibrary.org/obo/SO_0000097)

# File 'lib/biointerchange/so.rb', line 899

def self.nucleomorph_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000097')
end

.nucleomorphic_chromosome ⇒ Object

A chromosome originating in a nucleomorph. (http://purl.obolibrary.org/obo/SO_0000829)

# File 'lib/biointerchange/so.rb', line 5255

def self.nucleomorphic_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000829')
end

.nucleomorphic_sequence ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000739)

# File 'lib/biointerchange/so.rb', line 4757

def self.nucleomorphic_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000739')
end

.nucleotide_binding_site ⇒ Object

A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues. (http://purl.obolibrary.org/obo/SO_0001655)

# File 'lib/biointerchange/so.rb', line 10141

def self.nucleotide_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001655')
end

.nucleotide_match ⇒ Object

A match against a nucleotide sequence. (http://purl.obolibrary.org/obo/SO_0000347)

# File 'lib/biointerchange/so.rb', line 2403

def self.nucleotide_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000347')
end

.nucleotide_motif ⇒ Object

A region of nucleotide sequence corresponding to a known motif. (http://purl.obolibrary.org/obo/SO_0000714)

# File 'lib/biointerchange/so.rb', line 4607

def self.nucleotide_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000714')
end

.nucleotide_to_protein_binding_site ⇒ Object

A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. (http://purl.obolibrary.org/obo/SO_0001654)

# File 'lib/biointerchange/so.rb', line 10135

def self.nucleotide_to_protein_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001654')
end

.octamer_motif ⇒ Object

A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors. (http://purl.obolibrary.org/obo/SO_0001258)

# File 'lib/biointerchange/so.rb', line 7813

def self.octamer_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001258')
end

.Okazaki_fragment ⇒ Object

Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication. (http://purl.obolibrary.org/obo/SO_0001985)

# File 'lib/biointerchange/so.rb', line 12113

def self.Okazaki_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001985')
end

.oligo ⇒ Object

A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. (http://purl.obolibrary.org/obo/SO_0000696)

# File 'lib/biointerchange/so.rb', line 4499

def self.oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000696')
end

.oligo_U_tail ⇒ Object

The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602). (http://purl.obolibrary.org/obo/SO_0000609)

# File 'lib/biointerchange/so.rb', line 3977

def self.oligo_U_tail
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000609')
end

.one_methyl_three_three_amino_three_carboxypropyl_pseudouridine ⇒ Object

1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001373)

# File 'lib/biointerchange/so.rb', line 8503

def self.one_methyl_three_three_amino_three_carboxypropyl_pseudouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001373')
end

.one_methyladenosine ⇒ Object

1_methyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001295)

# File 'lib/biointerchange/so.rb', line 8035

def self.one_methyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001295')
end

.one_methylguanosine ⇒ Object

1_methylguanosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001324)

# File 'lib/biointerchange/so.rb', line 8209

def self.one_methylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001324')
end

.one_methylinosine ⇒ Object

1-methylinosine is a modified insosine. (http://purl.obolibrary.org/obo/SO_0001278)

# File 'lib/biointerchange/so.rb', line 7933

def self.one_methylinosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001278')
end

.one_methylpseudouridine ⇒ Object

1_methylpseudouridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001347)

# File 'lib/biointerchange/so.rb', line 8347

def self.one_methylpseudouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001347')
end

.one_two_prime_O_dimethyladenosine ⇒ Object

1,2'-O-dimethyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001314)

# File 'lib/biointerchange/so.rb', line 8149

def self.one_two_prime_O_dimethyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001314')
end

.one_two_prime_O_dimethylguanosine ⇒ Object

1_2prime_O_dimethylguanosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001340)

# File 'lib/biointerchange/so.rb', line 8305

def self.one_two_prime_O_dimethylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001340')
end

.one_two_prime_O_dimethylinosine ⇒ Object

1,2'-O-dimethylinosine is a modified inosine. (http://purl.obolibrary.org/obo/SO_0001279)

# File 'lib/biointerchange/so.rb', line 7939

def self.one_two_prime_O_dimethylinosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001279')
end

.open_chromatin_region ⇒ Object

A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA. (http://purl.obolibrary.org/obo/SO_0001747)

# File 'lib/biointerchange/so.rb', line 10693

def self.open_chromatin_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001747')
end

.operator ⇒ Object

A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon. (http://purl.obolibrary.org/obo/SO_0000057)

# File 'lib/biointerchange/so.rb', line 655

def self.operator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000057')
end

.operon ⇒ Object

A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region. (http://purl.obolibrary.org/obo/SO_0000178)

# File 'lib/biointerchange/so.rb', line 1385

def self.operon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000178')
end

.operon_member ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000080)

# File 'lib/biointerchange/so.rb', line 797

def self.operon_member
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000080')
end

.ORF ⇒ Object

The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER. (http://purl.obolibrary.org/obo/SO_0000236)

# File 'lib/biointerchange/so.rb', line 1737

def self.ORF
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000236')
end

.organelle_sequence ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000736)

# File 'lib/biointerchange/so.rb', line 4739

def self.organelle_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000736')
end

.oriC ⇒ Object

An origin of bacterial chromosome replication. (http://purl.obolibrary.org/obo/SO_0000953)

# File 'lib/biointerchange/so.rb', line 5999

def self.oriC
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000953')
end

.origin_of_replication ⇒ Object

The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies. (http://purl.obolibrary.org/obo/SO_0000296)

# File 'lib/biointerchange/so.rb', line 2097

def self.origin_of_replication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000296')
end

.oriT ⇒ Object

A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization. (http://purl.obolibrary.org/obo/SO_0000724)

# File 'lib/biointerchange/so.rb', line 4667

def self.oriT
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000724')
end

.oriV ⇒ Object

An origin of vegetative replication in plasmids and phages. (http://purl.obolibrary.org/obo/SO_0000952)

# File 'lib/biointerchange/so.rb', line 5993

def self.oriV
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000952')
end

.orphan ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000910)

# File 'lib/biointerchange/so.rb', line 5741

def self.orphan
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000910')
end

.orphan_CDS ⇒ Object

A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence. (http://purl.obolibrary.org/obo/SO_1001247)

# File 'lib/biointerchange/so.rb', line 13469

def self.orphan_CDS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001247')
end

.orthologous ⇒ Object

An attribute describing a kind of homology where divergence occured after a speciation event. (http://purl.obolibrary.org/obo/SO_0000858)

# File 'lib/biointerchange/so.rb', line 5429

def self.orthologous
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000858')
end

.orthologous_region ⇒ Object

A homologous_region that is orthologous to another region. (http://purl.obolibrary.org/obo/SO_0000855)

# File 'lib/biointerchange/so.rb', line 5411

def self.orthologous_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000855')
end

.orthologous_to ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#orthologous_to)

# File 'lib/biointerchange/so.rb', line 191

def self.orthologous_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#orthologous_to')
end

.outron ⇒ Object

A region of a primary transcript, that is removed via trans splicing. (http://purl.obolibrary.org/obo/SO_0001475)

# File 'lib/biointerchange/so.rb', line 9109

def self.outron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001475')
end

.overlapping ⇒ Object

An attribute describing a gene that has a sequence that overlaps the sequence of another gene. (http://purl.obolibrary.org/obo/SO_0000068)

# File 'lib/biointerchange/so.rb', line 725

def self.overlapping
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000068')
end

.overlapping_EST_set ⇒ Object

A continous experimental result region extending the length of multiple overlapping EST's. (http://purl.obolibrary.org/obo/SO_0001262)

# File 'lib/biointerchange/so.rb', line 7837

def self.overlapping_EST_set
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001262')
end

.overlapping_feature_set ⇒ Object

A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature. (http://purl.obolibrary.org/obo/SO_0001261)

# File 'lib/biointerchange/so.rb', line 7831

def self.overlapping_feature_set
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001261')
end

.overlaps ⇒ Object

X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y. (http://purl.obolibrary.org/obo/so_2_5_2.obo#overlaps)

# File 'lib/biointerchange/so.rb', line 197

def self.overlaps
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#overlaps')
end

.OxyS_RNA ⇒ Object

A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages. (http://purl.obolibrary.org/obo/SO_0000384)

# File 'lib/biointerchange/so.rb', line 2619

def self.OxyS_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000384')
end

.p_element ⇒ Object

A P_element is a DNA transposon responsible for hybrid dysgenesis. (http://purl.obolibrary.org/obo/SO_0001535)

# File 'lib/biointerchange/so.rb', line 9469

def self.p_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001535')
end

.PAC ⇒ Object

The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. (http://purl.obolibrary.org/obo/SO_0000154)

# File 'lib/biointerchange/so.rb', line 1241

def self.PAC
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000154')
end

.PAC_clone ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000762)

# File 'lib/biointerchange/so.rb', line 4895

def self.PAC_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000762')
end

.PAC_end ⇒ Object

A region of sequence from the end of a PAC clone that may provide a highly specific marker. (http://purl.obolibrary.org/obo/SO_0001480)

# File 'lib/biointerchange/so.rb', line 9139

def self.PAC_end
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001480')
end

.paired_end_fragment ⇒ Object

An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair). (http://purl.obolibrary.org/obo/SO_0001790)

# File 'lib/biointerchange/so.rb', line 10945

def self.paired_end_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001790')
end

.paracentric ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001519)

# File 'lib/biointerchange/so.rb', line 9373

def self.paracentric
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001519')
end

.paracentric_inversion ⇒ Object

A chromosomal inversion that does not include the centromere. (http://purl.obolibrary.org/obo/SO_1000047)

# File 'lib/biointerchange/so.rb', line 12713

def self.paracentric_inversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000047')
end

.parallel_beta_strand ⇒ Object

A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets. (http://purl.obolibrary.org/obo/SO_0001113)

# File 'lib/biointerchange/so.rb', line 6949

def self.parallel_beta_strand
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001113')
end

.paralogous ⇒ Object

An attribute describing a kind of homology where divergence occurred after a duplication event. (http://purl.obolibrary.org/obo/SO_0000859)

# File 'lib/biointerchange/so.rb', line 5435

def self.paralogous
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000859')
end

.paralogous_region ⇒ Object

A homologous_region that is paralogous to another region. (http://purl.obolibrary.org/obo/SO_0000854)

# File 'lib/biointerchange/so.rb', line 5405

def self.paralogous_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000854')
end

.paralogous_to ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#paralogous_to)

# File 'lib/biointerchange/so.rb', line 203

def self.paralogous_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#paralogous_to')
end

.part_of ⇒ Object

Either:

Example: amino_acid part_of polypeptide.
(http://purl.obolibrary.org/obo/part_of)

Or:

X part_of Y if X is a subregion of Y.
(http://purl.obolibrary.org/obo/so_2_5_2.obo#part_of)

# File 'lib/biointerchange/so.rb', line 11

def self.part_of
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/part_of'), RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#part_of') ]
end

.partial_evidence_for_feature ⇒ Object

B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A. (http://purl.obolibrary.org/obo/so_2_5_2.obo#partial_evidence_for_feature)

# File 'lib/biointerchange/so.rb', line 209

def self.partial_evidence_for_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#partial_evidence_for_feature')
end

.partial_genomic_sequence_assembly ⇒ Object

A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's. (http://purl.obolibrary.org/obo/SO_0001876)

# File 'lib/biointerchange/so.rb', line 11461

def self.partial_genomic_sequence_assembly
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001876')
end

.partially_characterised_chromosomal_mutation ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_1000175)

# File 'lib/biointerchange/so.rb', line 13331

def self.partially_characterised_chromosomal_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000175')
end

.partially_processed_cDNA_clone ⇒ Object

A cDNA invalidated clone by partial processing. (http://purl.obolibrary.org/obo/SO_0000813)

# File 'lib/biointerchange/so.rb', line 5171

def self.partially_processed_cDNA_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000813')
end

.paternal_uniparental_disomy ⇒ Object

Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother. (http://purl.obolibrary.org/obo/SO_0001746)

# File 'lib/biointerchange/so.rb', line 10687

def self.paternal_uniparental_disomy
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001746')
end

.paternal_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001776)

# File 'lib/biointerchange/so.rb', line 10867

def self.paternal_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001776')
end

.paternally_imprinted ⇒ Object

The paternal copy of the gene is modified, rendering it transcriptionally silent. (http://purl.obolibrary.org/obo/SO_0000136)

# File 'lib/biointerchange/so.rb', line 1133

def self.paternally_imprinted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000136')
end

.paternally_imprinted_gene ⇒ Object

A gene that is paternally imprinted. (http://purl.obolibrary.org/obo/SO_0000889)

# File 'lib/biointerchange/so.rb', line 5615

def self.paternally_imprinted_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000889')
end

.pathogenic_island ⇒ Object

Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species. (http://purl.obolibrary.org/obo/SO_0000773)

# File 'lib/biointerchange/so.rb', line 4955

def self.pathogenic_island
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000773')
end

.PCB ⇒ Object

A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle. (http://purl.obolibrary.org/obo/SO_0001871)

# File 'lib/biointerchange/so.rb', line 11431

def self.PCB
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001871')
end

.PCR_product ⇒ Object

A region amplified by a PCR reaction. (http://purl.obolibrary.org/obo/SO_0000006)

# File 'lib/biointerchange/so.rb', line 351

def self.PCR_product
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000006')
end

.pedigree_specific_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001779)

# File 'lib/biointerchange/so.rb', line 10885

def self.pedigree_specific_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001779')
end

.peptide_coil ⇒ Object

Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds). (http://purl.obolibrary.org/obo/SO_0100012)

# File 'lib/biointerchange/so.rb', line 12419

def self.peptide_coil
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100012')
end

.peptide_collection ⇒ Object

A collection of peptide sequences. (http://purl.obolibrary.org/obo/SO_0001501)

# File 'lib/biointerchange/so.rb', line 9265

def self.peptide_collection
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001501')
end

.peptide_helix ⇒ Object

A helix is a secondary_structure conformation where the peptide backbone forms a coil. (http://purl.obolibrary.org/obo/SO_0001114)

# File 'lib/biointerchange/so.rb', line 6955

def self.peptide_helix
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001114')
end

.peptide_localization_signal ⇒ Object

A region of peptide sequence used to target the polypeptide molecule to a specific organelle. (http://purl.obolibrary.org/obo/SO_0001527)

# File 'lib/biointerchange/so.rb', line 9421

def self.peptide_localization_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001527')
end

.peptidyl ⇒ Object

An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds. (http://purl.obolibrary.org/obo/SO_0001407)

# File 'lib/biointerchange/so.rb', line 8707

def self.peptidyl
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001407')
end

.pericentric ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001518)

# File 'lib/biointerchange/so.rb', line 9367

def self.pericentric
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001518')
end

.pericentric_inversion ⇒ Object

A chromosomal inversion that includes the centromere. (http://purl.obolibrary.org/obo/SO_1000046)

# File 'lib/biointerchange/so.rb', line 12707

def self.pericentric_inversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000046')
end

.peroxywybutosine ⇒ Object

Peroxywybutosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001333)

# File 'lib/biointerchange/so.rb', line 8263

def self.peroxywybutosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001333')
end

.Phage_RNA_Polymerase_Promoter ⇒ Object

A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription. (http://purl.obolibrary.org/obo/SO_0001204)

# File 'lib/biointerchange/so.rb', line 7495

def self.Phage_RNA_Polymerase_Promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001204')
end

.phage_sequence ⇒ Object

The nucleotide sequence of a virus that infects bacteria. (http://purl.obolibrary.org/obo/SO_0001042)

# File 'lib/biointerchange/so.rb', line 6527

def self.phage_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001042')
end

.phagemid ⇒ Object

A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with "helper" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids. (SO:ma) (http://purl.obolibrary.org/obo/SO_0000157)

# File 'lib/biointerchange/so.rb', line 1259

def self.phagemid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000157')
end

.phagemid_clone ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000761)

# File 'lib/biointerchange/so.rb', line 4889

def self.phagemid_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000761')
end

.phenylalanine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001441)

# File 'lib/biointerchange/so.rb', line 8905

def self.phenylalanine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001441')
end

.phenylalanine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding phenylalanyl tRNA (SO:0000267). (http://purl.obolibrary.org/obo/SO_0000224)

# File 'lib/biointerchange/so.rb', line 1665

def self.phenylalanine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000224')
end

.phenylalanyl_tRNA ⇒ Object

A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region. (http://purl.obolibrary.org/obo/SO_0000267)

# File 'lib/biointerchange/so.rb', line 1923

def self.phenylalanyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000267')
end

.phosphorylation_site ⇒ Object

A post-translationally modified region in which residues of the protein are modified by phosphorylation. (http://purl.obolibrary.org/obo/SO_0001811)

# File 'lib/biointerchange/so.rb', line 11071

def self.phosphorylation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001811')
end

.pi_helix ⇒ Object

The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier. (http://purl.obolibrary.org/obo/SO_0001118)

# File 'lib/biointerchange/so.rb', line 6979

def self.pi_helix
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001118')
end

.PIP_box ⇒ Object

A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains. (http://purl.obolibrary.org/obo/SO_0001810)

# File 'lib/biointerchange/so.rb', line 11065

def self.PIP_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001810')
end

.piRNA ⇒ Object

A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements. (http://purl.obolibrary.org/obo/SO_0001035)

# File 'lib/biointerchange/so.rb', line 6485

def self.piRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001035')
end

.piRNA_gene ⇒ Object

A gene that encodes for an piwi associated RNA. (http://purl.obolibrary.org/obo/SO_0001638)

# File 'lib/biointerchange/so.rb', line 10063

def self.piRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001638')
end

.plasmid ⇒ Object

A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism. (http://purl.obolibrary.org/obo/SO_0000155)

# File 'lib/biointerchange/so.rb', line 1247

def self.plasmid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000155')
end

.plasmid_clone ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000759)

# File 'lib/biointerchange/so.rb', line 4877

def self.plasmid_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000759')
end

.plasmid_gene ⇒ Object

A gene from plasmid sequence. (http://purl.obolibrary.org/obo/SO_0000098)

# File 'lib/biointerchange/so.rb', line 905

def self.plasmid_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000098')
end

.plasmid_location ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000749)

# File 'lib/biointerchange/so.rb', line 4817

def self.plasmid_location
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000749')
end

.plasmid_vector ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000755)

# File 'lib/biointerchange/so.rb', line 4853

def self.plasmid_vector
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000755')
end

.plastid_gene ⇒ Object

A gene from plastid sequence. (http://purl.obolibrary.org/obo/SO_0000090)

# File 'lib/biointerchange/so.rb', line 857

def self.plastid_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000090')
end

.plastid_sequence ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000740)

# File 'lib/biointerchange/so.rb', line 4763

def self.plastid_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000740')
end

.plus_1_frameshift ⇒ Object

A frameshift caused by inserting one base. (http://purl.obolibrary.org/obo/SO_0000868)

# File 'lib/biointerchange/so.rb', line 5489

def self.plus_1_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000868')
end

.plus_1_frameshift_variant ⇒ Object

A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward. (http://purl.obolibrary.org/obo/SO_0001594)

# File 'lib/biointerchange/so.rb', line 9805

def self.plus_1_frameshift_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001594')
end

.plus_1_translational_frameshift ⇒ Object

The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. (http://purl.obolibrary.org/obo/SO_0001211)

# File 'lib/biointerchange/so.rb', line 7537

def self.plus_1_translational_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001211')
end

.plus_1_translationally_frameshifted ⇒ Object

An attribute describing a translational frameshift of +1. (http://purl.obolibrary.org/obo/SO_1001263)

# File 'lib/biointerchange/so.rb', line 13523

def self.plus_1_translationally_frameshifted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001263')
end

.plus_2_frameshift_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001595)

# File 'lib/biointerchange/so.rb', line 9811

def self.plus_2_frameshift_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001595')
end

.plus_2_framshift ⇒ Object

A frameshift caused by inserting two bases. (http://purl.obolibrary.org/obo/SO_0000869)

# File 'lib/biointerchange/so.rb', line 5495

def self.plus_2_framshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000869')
end

.plus_2_translational_frameshift ⇒ Object

The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. (http://purl.obolibrary.org/obo/SO_0001212)

# File 'lib/biointerchange/so.rb', line 7543

def self.plus_2_translational_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001212')
end

.PNA ⇒ Object

An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds. (http://purl.obolibrary.org/obo/SO_0001184)

# File 'lib/biointerchange/so.rb', line 7375

def self.PNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001184')
end

.PNA_oligo ⇒ Object

Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds. (http://purl.obolibrary.org/obo/SO_0001011)

# File 'lib/biointerchange/so.rb', line 6341

def self.PNA_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001011')
end

.point_centromere ⇒ Object

A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae. (http://purl.obolibrary.org/obo/SO_0001794)

# File 'lib/biointerchange/so.rb', line 10969

def self.point_centromere
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001794')
end

.point_mutation ⇒ Object

A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. (http://purl.obolibrary.org/obo/SO_1000008)

# File 'lib/biointerchange/so.rb', line 12491

def self.point_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000008')
end

.polinton ⇒ Object

A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements. (http://purl.obolibrary.org/obo/SO_0001170)

# File 'lib/biointerchange/so.rb', line 7291

def self.polinton
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001170')
end

.polyA_primed_cDNA_clone ⇒ Object

A cDNA clone invalidated by polyA priming. (http://purl.obolibrary.org/obo/SO_0000812)

# File 'lib/biointerchange/so.rb', line 5165

def self.polyA_primed_cDNA_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000812')
end

.polyA_sequence ⇒ Object

Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs. (http://purl.obolibrary.org/obo/SO_0000610)

# File 'lib/biointerchange/so.rb', line 3983

def self.polyA_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000610')
end

.polyA_signal_sequence ⇒ Object

The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA. (http://purl.obolibrary.org/obo/SO_0000551)

# File 'lib/biointerchange/so.rb', line 3625

def self.polyA_signal_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000551')
end

.polyA_site ⇒ Object

The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence. (http://purl.obolibrary.org/obo/SO_0000553)

# File 'lib/biointerchange/so.rb', line 3637

def self.polyA_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000553')
end

.polyadenylated ⇒ Object

A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule. (http://purl.obolibrary.org/obo/SO_0000246)

# File 'lib/biointerchange/so.rb', line 1797

def self.polyadenylated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000246')
end

.polyadenylated_mRNA ⇒ Object

An mRNA that is polyadenylated. (http://purl.obolibrary.org/obo/SO_0000871)

# File 'lib/biointerchange/so.rb', line 5507

def self.polyadenylated_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000871')
end

.polyadenylation_variant ⇒ Object

A sequence variant that changes polyadenylation with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001545)

# File 'lib/biointerchange/so.rb', line 9529

def self.polyadenylation_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001545')
end

.polycistronic ⇒ Object

An attribute describing a sequence that contains the code for more than one gene product. (http://purl.obolibrary.org/obo/SO_0000880)

# File 'lib/biointerchange/so.rb', line 5561

def self.polycistronic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000880')
end

.polycistronic_gene ⇒ Object

A gene that is polycistronic. (http://purl.obolibrary.org/obo/SO_0000477)

# File 'lib/biointerchange/so.rb', line 3181

def self.polycistronic_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000477')
end

.polycistronic_mRNA ⇒ Object

An mRNA that encodes multiple proteins from at least two non-overlapping regions. (http://purl.obolibrary.org/obo/SO_0000634)

# File 'lib/biointerchange/so.rb', line 4127

def self.polycistronic_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000634')
end

.polycistronic_primary_transcript ⇒ Object

A primary transcript encoding for more than one gene product. (http://purl.obolibrary.org/obo/SO_0000631)

# File 'lib/biointerchange/so.rb', line 4109

def self.polycistronic_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000631')
end

.polycistronic_transcript ⇒ Object

A transcript that is polycistronic. (http://purl.obolibrary.org/obo/SO_0000078)

# File 'lib/biointerchange/so.rb', line 785

def self.polycistronic_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000078')
end

.polymer_attribute ⇒ Object

An attribute to describe the kind of biological sequence. (http://purl.obolibrary.org/obo/SO_0000443)

# File 'lib/biointerchange/so.rb', line 2977

def self.polymer_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000443')
end

.polymerase_synthesis_read ⇒ Object

A read produced by the polymerase based sequence by synthesis method. (http://purl.obolibrary.org/obo/SO_0001426)

# File 'lib/biointerchange/so.rb', line 8821

def self.polymerase_synthesis_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001426')
end

.polymorphic_pseudogene ⇒ Object

Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated. (http://purl.obolibrary.org/obo/SO_0001841)

# File 'lib/biointerchange/so.rb', line 11251

def self.polymorphic_pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001841')
end

.polymorphic_sequence_variant ⇒ Object

A sequence variant that is segregating in one or more natural populations of a species. (http://purl.obolibrary.org/obo/SO_0001025)

# File 'lib/biointerchange/so.rb', line 6425

def self.polymorphic_sequence_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001025')
end

.polymorphic_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001766)

# File 'lib/biointerchange/so.rb', line 10807

def self.polymorphic_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001766')
end

.polypeptide ⇒ Object

A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. (http://purl.obolibrary.org/obo/SO_0000104)

# File 'lib/biointerchange/so.rb', line 941

def self.polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000104')
end

.polypeptide_binding_motif ⇒ Object

A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand. (http://purl.obolibrary.org/obo/SO_0100018)

# File 'lib/biointerchange/so.rb', line 12455

def self.polypeptide_binding_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100018')
end

.polypeptide_calcium_ion_contact_site ⇒ Object

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions. (http://purl.obolibrary.org/obo/SO_0001094)

# File 'lib/biointerchange/so.rb', line 6835

def self.polypeptide_calcium_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001094')
end

.polypeptide_catalytic_motif ⇒ Object

A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues. (http://purl.obolibrary.org/obo/SO_0100019)

# File 'lib/biointerchange/so.rb', line 12461

def self.polypeptide_catalytic_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100019')
end

.polypeptide_cobalt_ion_contact_site ⇒ Object

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions. (http://purl.obolibrary.org/obo/SO_0001095)

# File 'lib/biointerchange/so.rb', line 6841

def self.polypeptide_cobalt_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001095')
end

.polypeptide_conserved_motif ⇒ Object

A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found. (http://purl.obolibrary.org/obo/SO_0100017)

# File 'lib/biointerchange/so.rb', line 12449

def self.polypeptide_conserved_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100017')
end

.polypeptide_conserved_region ⇒ Object

A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found. (http://purl.obolibrary.org/obo/SO_0100021)

# File 'lib/biointerchange/so.rb', line 12473

def self.polypeptide_conserved_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100021')
end

.polypeptide_copper_ion_contact_site ⇒ Object

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions. (http://purl.obolibrary.org/obo/SO_0001096)

# File 'lib/biointerchange/so.rb', line 6847

def self.polypeptide_copper_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001096')
end

.polypeptide_DNA_contact ⇒ Object

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA. (http://purl.obolibrary.org/obo/SO_0100020)

# File 'lib/biointerchange/so.rb', line 12467

def self.polypeptide_DNA_contact
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100020')
end

.polypeptide_domain ⇒ Object

A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution. (http://purl.obolibrary.org/obo/SO_0000417)

# File 'lib/biointerchange/so.rb', line 2817

def self.polypeptide_domain
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000417')
end

.polypeptide_function_variant ⇒ Object

A sequence variant which changes polypeptide functioning with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001554)

# File 'lib/biointerchange/so.rb', line 9583

def self.polypeptide_function_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001554')
end

.polypeptide_fusion ⇒ Object

A sequence variant that causes a fusion of two polypeptide sequences. (http://purl.obolibrary.org/obo/SO_0001616)

# File 'lib/biointerchange/so.rb', line 9937

def self.polypeptide_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001616')
end

.polypeptide_gain_of_function_variant ⇒ Object

A sequence variant which causes gain of polypeptide function with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001557)

# File 'lib/biointerchange/so.rb', line 9601

def self.polypeptide_gain_of_function_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001557')
end

.polypeptide_iron_ion_contact_site ⇒ Object

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions. (http://purl.obolibrary.org/obo/SO_0001097)

# File 'lib/biointerchange/so.rb', line 6853

def self.polypeptide_iron_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001097')
end

.polypeptide_ligand_contact ⇒ Object

Residues which interact with a ligand. (http://purl.obolibrary.org/obo/SO_0001105)

# File 'lib/biointerchange/so.rb', line 6901

def self.polypeptide_ligand_contact
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001105')
end

.polypeptide_localization_variant ⇒ Object

A sequence variant which changes the localization of a polypeptide with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001558)

# File 'lib/biointerchange/so.rb', line 9607

def self.polypeptide_localization_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001558')
end

.polypeptide_loss_of_function_variant ⇒ Object

A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001559)

# File 'lib/biointerchange/so.rb', line 9613

def self.polypeptide_loss_of_function_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001559')
end

.polypeptide_magnesium_ion_contact_site ⇒ Object

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions. (http://purl.obolibrary.org/obo/SO_0001098)

# File 'lib/biointerchange/so.rb', line 6859

def self.polypeptide_magnesium_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001098')
end

.polypeptide_manganese_ion_contact_site ⇒ Object

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions. (http://purl.obolibrary.org/obo/SO_0001099)

# File 'lib/biointerchange/so.rb', line 6865

def self.polypeptide_manganese_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001099')
end

.polypeptide_metal_contact ⇒ Object

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions. (http://purl.obolibrary.org/obo/SO_0001092)

# File 'lib/biointerchange/so.rb', line 6823

def self.polypeptide_metal_contact
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001092')
end

.polypeptide_molybdenum_ion_contact_site ⇒ Object

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions. (http://purl.obolibrary.org/obo/SO_0001100)

# File 'lib/biointerchange/so.rb', line 6871

def self.polypeptide_molybdenum_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001100')
end

.polypeptide_motif ⇒ Object

A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.). (http://purl.obolibrary.org/obo/SO_0001067)

# File 'lib/biointerchange/so.rb', line 6679

def self.polypeptide_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001067')
end

.polypeptide_nest_left_right_motif ⇒ Object

A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. (http://purl.obolibrary.org/obo/SO_0001121)

# File 'lib/biointerchange/so.rb', line 6997

def self.polypeptide_nest_left_right_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001121')
end

.polypeptide_nest_motif ⇒ Object

A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops. (http://purl.obolibrary.org/obo/SO_0001120)

# File 'lib/biointerchange/so.rb', line 6991

def self.polypeptide_nest_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001120')
end

.polypeptide_nest_right_left_motif ⇒ Object

A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. (http://purl.obolibrary.org/obo/SO_0001122)

# File 'lib/biointerchange/so.rb', line 7003

def self.polypeptide_nest_right_left_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001122')
end

.polypeptide_nickel_ion_contact_site ⇒ Object

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions. (http://purl.obolibrary.org/obo/SO_0001101)

# File 'lib/biointerchange/so.rb', line 6877

def self.polypeptide_nickel_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001101')
end

.polypeptide_partial_loss_of_function ⇒ Object

A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001561)

# File 'lib/biointerchange/so.rb', line 9625

def self.polypeptide_partial_loss_of_function
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001561')
end

.polypeptide_post_translational_processing_affected ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_1000123)

# File 'lib/biointerchange/so.rb', line 13121

def self.polypeptide_post_translational_processing_affected
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000123')
end

.polypeptide_post_translational_processing_variant ⇒ Object

A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001562)

# File 'lib/biointerchange/so.rb', line 9631

def self.polypeptide_post_translational_processing_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001562')
end

.polypeptide_region ⇒ Object

Biological sequence region that can be assigned to a specific subsequence of a polypeptide. (http://purl.obolibrary.org/obo/SO_0000839)

# File 'lib/biointerchange/so.rb', line 5315

def self.polypeptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000839')
end

.polypeptide_repeat ⇒ Object

A polypeptide_repeat is a single copy of an internal sequence repetition. (http://purl.obolibrary.org/obo/SO_0001068)

# File 'lib/biointerchange/so.rb', line 6685

def self.polypeptide_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001068')
end

.polypeptide_secondary_structure ⇒ Object

A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain. (http://purl.obolibrary.org/obo/SO_0001078)

# File 'lib/biointerchange/so.rb', line 6739

def self.polypeptide_secondary_structure
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001078')
end

.polypeptide_sequence_variant ⇒ Object

A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence. (http://purl.obolibrary.org/obo/SO_0001603)

# File 'lib/biointerchange/so.rb', line 9859

def self.polypeptide_sequence_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001603')
end

.polypeptide_sequencing_information ⇒ Object

Incompatibility in the sequence due to some experimental problem. (http://purl.obolibrary.org/obo/SO_0001082)

# File 'lib/biointerchange/so.rb', line 6763

def self.polypeptide_sequencing_information
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001082')
end

.polypeptide_structural_motif ⇒ Object

Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit. (http://purl.obolibrary.org/obo/SO_0001079)

# File 'lib/biointerchange/so.rb', line 6745

def self.polypeptide_structural_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001079')
end

.polypeptide_structural_region ⇒ Object

Region of polypeptide with a given structural property. (http://purl.obolibrary.org/obo/SO_0001070)

# File 'lib/biointerchange/so.rb', line 6691

def self.polypeptide_structural_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001070')
end

.polypeptide_truncation ⇒ Object

A sequence variant of the CD that causes a truncation of the resulting polypeptide. (http://purl.obolibrary.org/obo/SO_0001617)

# File 'lib/biointerchange/so.rb', line 9943

def self.polypeptide_truncation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001617')
end

.polypeptide_tungsten_ion_contact_site ⇒ Object

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions. (http://purl.obolibrary.org/obo/SO_0001102)

# File 'lib/biointerchange/so.rb', line 6883

def self.polypeptide_tungsten_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001102')
end

.polypeptide_turn_motif ⇒ Object

A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues. (http://purl.obolibrary.org/obo/SO_0001128)

# File 'lib/biointerchange/so.rb', line 7039

def self.polypeptide_turn_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001128')
end

.polypeptide_variation_site ⇒ Object

A site of sequence variation (alteration). Alternative sequence due to naturally occuring events such as polymorphisms and altermatve splicing or experimental methods such as site directed mutagenesis. (http://purl.obolibrary.org/obo/SO_0001146)

# File 'lib/biointerchange/so.rb', line 7147

def self.polypeptide_variation_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001146')
end

.polypeptide_zinc_ion_contact_site ⇒ Object

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions. (http://purl.obolibrary.org/obo/SO_0001103)

# File 'lib/biointerchange/so.rb', line 6889

def self.polypeptide_zinc_ion_contact_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001103')
end

.polyploid ⇒ Object

A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number. (http://purl.obolibrary.org/obo/SO_0001254)

# File 'lib/biointerchange/so.rb', line 7789

def self.polyploid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001254')
end

.polypyrimidine_tract ⇒ Object

The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing. (http://purl.obolibrary.org/obo/SO_0000612)

# File 'lib/biointerchange/so.rb', line 3995

def self.polypyrimidine_tract
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000612')
end

.population_specific_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001780)

# File 'lib/biointerchange/so.rb', line 10891

def self.population_specific_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001780')
end

.position_of ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#position_of)

# File 'lib/biointerchange/so.rb', line 215

def self.position_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#position_of')
end

.positional_candidate_gene ⇒ Object

A candidate gene whose association with a trait is based on the gene's location on a chromosome. (http://purl.obolibrary.org/obo/SO_0001868)

# File 'lib/biointerchange/so.rb', line 11413

def self.positional_candidate_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001868')
end

.positive_sense_ssRNA_viral_sequence ⇒ Object

A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host. (http://purl.obolibrary.org/obo/SO_0001201)

# File 'lib/biointerchange/so.rb', line 7477

def self.positive_sense_ssRNA_viral_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001201')
end

.positively_autoregulated ⇒ Object

The gene product is involved in its own transcriptional regulation, where it increases transcription. (http://purl.obolibrary.org/obo/SO_0000475)

# File 'lib/biointerchange/so.rb', line 3169

def self.positively_autoregulated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000475')
end

.positively_autoregulated_gene ⇒ Object

A gene that is positively autoregulated. (http://purl.obolibrary.org/obo/SO_0000892)

# File 'lib/biointerchange/so.rb', line 5633

def self.positively_autoregulated_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000892')
end

.possible_assembly_error ⇒ Object

A region of sequence where there may have been an error in the assembly. (http://purl.obolibrary.org/obo/SO_0000702)

# File 'lib/biointerchange/so.rb', line 4535

def self.possible_assembly_error
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000702')
end

.possible_base_call_error ⇒ Object

A region of sequence where the validity of the base calling is questionable. (http://purl.obolibrary.org/obo/SO_0000701)

# File 'lib/biointerchange/so.rb', line 4529

def self.possible_base_call_error
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000701')
end

.post_translationally_modified_region ⇒ Object

A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein. (http://purl.obolibrary.org/obo/SO_0001089)

# File 'lib/biointerchange/so.rb', line 6805

def self.post_translationally_modified_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001089')
end

.post_translationally_regulated ⇒ Object

An attribute describing a gene that is regulated after it has been translated. (http://purl.obolibrary.org/obo/SO_0000130)

# File 'lib/biointerchange/so.rb', line 1097

def self.post_translationally_regulated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000130')
end

.post_translationally_regulated_by_protein_modification ⇒ Object

An attribute describing a gene sequence where the resulting protein is modified to regulate it. (http://purl.obolibrary.org/obo/SO_0000469)

# File 'lib/biointerchange/so.rb', line 3133

def self.post_translationally_regulated_by_protein_modification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000469')
end

.post_translationally_regulated_by_protein_stability ⇒ Object

An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein. (http://purl.obolibrary.org/obo/SO_0000467)

# File 'lib/biointerchange/so.rb', line 3121

def self.post_translationally_regulated_by_protein_stability
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000467')
end

.post_translationally_regulated_gene ⇒ Object

A gene that is post translationally regulated. (http://purl.obolibrary.org/obo/SO_0000890)

# File 'lib/biointerchange/so.rb', line 5621

def self.post_translationally_regulated_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000890')
end

.pre_edited_mRNA ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000932)

# File 'lib/biointerchange/so.rb', line 5873

def self.pre_edited_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000932')
end

.pre_edited_region ⇒ Object

The region of a transcript that will be edited. (http://purl.obolibrary.org/obo/SO_0000583)

# File 'lib/biointerchange/so.rb', line 3821

def self.pre_edited_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000583')
end

.pre_miRNA ⇒ Object

The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin sructure. (http://purl.obolibrary.org/obo/SO_0001244)

# File 'lib/biointerchange/so.rb', line 7729

def self.pre_miRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001244')
end

.predicted ⇒ Object

An attribute describing an unverified region. (http://purl.obolibrary.org/obo/SO_0000732)

# File 'lib/biointerchange/so.rb', line 4715

def self.predicted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000732')
end

.predicted_ab_initio_computation ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000310)

# File 'lib/biointerchange/so.rb', line 2181

def self.predicted_ab_initio_computation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000310')
end

.predicted_by_ab_initio_computation ⇒ Object

An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity. (http://purl.obolibrary.org/obo/SO_0000911)

# File 'lib/biointerchange/so.rb', line 5747

def self.predicted_by_ab_initio_computation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000911')
end

.predicted_gene ⇒ Object

This term is mapped to MGED. Do not obsolete without consulting MGED ontology. (http://purl.obolibrary.org/obo/SO_0000996)

# File 'lib/biointerchange/so.rb', line 6251

def self.predicted_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000996')
end

.primary_transcript ⇒ Object

A transcript that in its initial state requires modification to be functional. (http://purl.obolibrary.org/obo/SO_0000185)

# File 'lib/biointerchange/so.rb', line 1431

def self.primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000185')
end

.primary_transcript_attribute ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000144)

# File 'lib/biointerchange/so.rb', line 1181

def self.primary_transcript_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000144')
end

.primary_transcript_region ⇒ Object

A part of a primary transcript. (http://purl.obolibrary.org/obo/SO_0000835)

# File 'lib/biointerchange/so.rb', line 5291

def self.primary_transcript_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000835')
end

.primer ⇒ Object

An oligo to which new deoxyribonucleotides can be added by DNA polymerase. (http://purl.obolibrary.org/obo/SO_0000112)

# File 'lib/biointerchange/so.rb', line 989

def self.primer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000112')
end

.primer_binding_site ⇒ Object

Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription. (http://purl.obolibrary.org/obo/SO_0005850)

# File 'lib/biointerchange/so.rb', line 12299

def self.primer_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005850')
end

.primer_match ⇒ Object

A nucleotide match to a primer sequence. (http://purl.obolibrary.org/obo/SO_0001472)

# File 'lib/biointerchange/so.rb', line 9091

def self.primer_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001472')
end

.probe ⇒ Object

A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid. (http://purl.obolibrary.org/obo/SO_0000051)

# File 'lib/biointerchange/so.rb', line 615

def self.probe
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000051')
end

.processed ⇒ Object

An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail. (http://purl.obolibrary.org/obo/SO_0000900)

# File 'lib/biointerchange/so.rb', line 5681

def self.processed
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000900')
end

.processed_from ⇒ Object

Inverse of processed_into. (http://purl.obolibrary.org/obo/so_2_5_2.obo#processed_from)

# File 'lib/biointerchange/so.rb', line 221

def self.processed_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#processed_from')
end

.processed_into ⇒ Object

X is processed_into Y if a region X is modified to create Y. (http://purl.obolibrary.org/obo/so_2_5_2.obo#processed_into)

# File 'lib/biointerchange/so.rb', line 227

def self.processed_into
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#processed_into')
end

.processed_pseudogene ⇒ Object

A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail. (http://purl.obolibrary.org/obo/SO_0000043)

# File 'lib/biointerchange/so.rb', line 567

def self.processed_pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000043')
end

.processed_transcript ⇒ Object

A transcript for which no open reading frame has been identified and for which no other function has been determined. (http://purl.obolibrary.org/obo/SO_0001503)

# File 'lib/biointerchange/so.rb', line 9277

def self.processed_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001503')
end

.processed_transcript_attribute ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000082)

# File 'lib/biointerchange/so.rb', line 809

def self.processed_transcript_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000082')
end

.proline ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001439)

# File 'lib/biointerchange/so.rb', line 8893

def self.proline
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001439')
end

.proline_tRNA_primary_transcript ⇒ Object

A primary transcript encoding prolyl tRNA (SO:0000268). (http://purl.obolibrary.org/obo/SO_0000225)

# File 'lib/biointerchange/so.rb', line 1671

def self.proline_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000225')
end

.prolyl_tRNA ⇒ Object

A tRNA sequence that has a proline anticodon, and a 3' proline binding region. (http://purl.obolibrary.org/obo/SO_0000268)

# File 'lib/biointerchange/so.rb', line 1929

def self.prolyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000268')
end

.promoter ⇒ Object

A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. (http://purl.obolibrary.org/obo/SO_0000167)

# File 'lib/biointerchange/so.rb', line 1319

def self.promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000167')
end

.promoter_element ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001659)

# File 'lib/biointerchange/so.rb', line 10165

def self.promoter_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001659')
end

.promoter_flanking_region ⇒ Object

A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites. (http://purl.obolibrary.org/obo/SO_0001952)

# File 'lib/biointerchange/so.rb', line 11917

def self.promoter_flanking_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001952')
end

.promoter_region ⇒ Object

A region of sequence which is part of a promoter. (http://purl.obolibrary.org/obo/SO_0000832)

# File 'lib/biointerchange/so.rb', line 5273

def self.promoter_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000832')
end

.promoter_targeting_sequence ⇒ Object

A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter. (http://purl.obolibrary.org/obo/SO_0001058)

# File 'lib/biointerchange/so.rb', line 6631

def self.promoter_targeting_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001058')
end

.promoter_trap_construct ⇒ Object

A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic. (http://purl.obolibrary.org/obo/SO_0001478)

# File 'lib/biointerchange/so.rb', line 9127

def self.promoter_trap_construct
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001478')
end

.propeptide ⇒ Object

Part of a peptide chain which is cleaved off during the formation of the mature protein. (http://purl.obolibrary.org/obo/SO_0001062)

# File 'lib/biointerchange/so.rb', line 6655

def self.propeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001062')
end

.propeptide_cleavage_site ⇒ Object

The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs. (http://purl.obolibrary.org/obo/SO_0001061)

# File 'lib/biointerchange/so.rb', line 6649

def self.propeptide_cleavage_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001061')
end

.prophage ⇒ Object

A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated "island". (GOC:jl) (http://purl.obolibrary.org/obo/SO_0001006)

# File 'lib/biointerchange/so.rb', line 6311

def self.prophage
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001006')
end

.proplastid_gene ⇒ Object

A gene from proplastid sequence. (http://purl.obolibrary.org/obo/SO_0000096)

# File 'lib/biointerchange/so.rb', line 893

def self.proplastid_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000096')
end

.proplastid_sequence ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000748)

# File 'lib/biointerchange/so.rb', line 4811

def self.proplastid_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000748')
end

.protease_site ⇒ Object

A polypeptide_region that codes for a protease cleavage site. (http://purl.obolibrary.org/obo/SO_0001956)

# File 'lib/biointerchange/so.rb', line 11941

def self.protease_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001956')
end

.protein_altering_variant ⇒ Object

A sequence_variant which is predicted to change the protein encoded in the coding sequence. (http://purl.obolibrary.org/obo/SO_0001818)

# File 'lib/biointerchange/so.rb', line 11113

def self.protein_altering_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001818')
end

.protein_binding_site ⇒ Object

A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules. (http://purl.obolibrary.org/obo/SO_0000410)

# File 'lib/biointerchange/so.rb', line 2775

def self.protein_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000410')
end

.protein_coding ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000010)

# File 'lib/biointerchange/so.rb', line 375

def self.protein_coding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000010')
end

.protein_coding_gene ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001217)

# File 'lib/biointerchange/so.rb', line 7573

def self.protein_coding_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001217')
end

.protein_coding_primary_transcript ⇒ Object

A primary transcript that, at least in part, encodes one or more proteins. (http://purl.obolibrary.org/obo/SO_0000120)

# File 'lib/biointerchange/so.rb', line 1037

def self.protein_coding_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000120')
end

.protein_hmm_match ⇒ Object

A match to a protein HMM such as pfam. (http://purl.obolibrary.org/obo/SO_0001831)

# File 'lib/biointerchange/so.rb', line 11191

def self.protein_hmm_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001831')
end

.protein_match ⇒ Object

A match against a protein sequence. (http://purl.obolibrary.org/obo/SO_0000349)

# File 'lib/biointerchange/so.rb', line 2415

def self.protein_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000349')
end

.protein_protein_contact ⇒ Object

A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues. (http://purl.obolibrary.org/obo/SO_0001093)

# File 'lib/biointerchange/so.rb', line 6829

def self.protein_protein_contact
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001093')
end

.protein_stability_element ⇒ Object

A polypeptide region that proves structure in a protein that affects the stability of the protein. (http://purl.obolibrary.org/obo/SO_0001955)

# File 'lib/biointerchange/so.rb', line 11935

def self.protein_stability_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001955')
end

.proviral_gene ⇒ Object

A gene from proviral sequence. (http://purl.obolibrary.org/obo/SO_0000099)

# File 'lib/biointerchange/so.rb', line 911

def self.proviral_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000099')
end

.proviral_location ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000751)

# File 'lib/biointerchange/so.rb', line 4829

def self.proviral_location
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000751')
end

.proviral_region ⇒ Object

A viral sequence which has integrated into a host genome. (http://purl.obolibrary.org/obo/SO_0000113)

# File 'lib/biointerchange/so.rb', line 995

def self.proviral_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000113')
end

.proximal_promoter_element ⇒ Object

DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor). (http://purl.obolibrary.org/obo/SO_0001668)

# File 'lib/biointerchange/so.rb', line 10219

def self.proximal_promoter_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001668')
end

.PSE_motif ⇒ Object

A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G). (http://purl.obolibrary.org/obo/SO_0000017)

# File 'lib/biointerchange/so.rb', line 417

def self.PSE_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000017')
end

.pseudogene ⇒ Object

A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog). (http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html) (http://purl.obolibrary.org/obo/SO_0000336)

# File 'lib/biointerchange/so.rb', line 2337

def self.pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000336')
end

.pseudogene_attribute ⇒ Object

An attribute of a pseudogene (SO:0000336). (http://purl.obolibrary.org/obo/SO_0000042)

# File 'lib/biointerchange/so.rb', line 561

def self.pseudogene_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000042')
end

.pseudogene_by_unequal_crossing_over ⇒ Object

A pseudogene caused by unequal crossing over at recombination. (http://purl.obolibrary.org/obo/SO_0000044)

# File 'lib/biointerchange/so.rb', line 573

def self.pseudogene_by_unequal_crossing_over
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000044')
end

.pseudogenic_exon ⇒ Object

A non functional descendant of an exon, part of a pseudogene. (http://purl.obolibrary.org/obo/SO_0000507)

# File 'lib/biointerchange/so.rb', line 3361

def self.pseudogenic_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000507')
end

.pseudogenic_gene_segment ⇒ Object

A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product. (http://purl.obolibrary.org/obo/SO_0001741)

# File 'lib/biointerchange/so.rb', line 10657

def self.pseudogenic_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001741')
end

.pseudogenic_region ⇒ Object

A non-functional descendent of a functional entity. (http://purl.obolibrary.org/obo/SO_0000462)

# File 'lib/biointerchange/so.rb', line 3091

def self.pseudogenic_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000462')
end

.pseudogenic_rRNA ⇒ Object

A non functional descendent of an rRNA. (http://purl.obolibrary.org/obo/SO_0000777)

# File 'lib/biointerchange/so.rb', line 4979

def self.pseudogenic_rRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000777')
end

.pseudogenic_transcript ⇒ Object

A non functional descendant of a transcript, part of a pseudogene. (http://purl.obolibrary.org/obo/SO_0000516)

# File 'lib/biointerchange/so.rb', line 3415

def self.pseudogenic_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000516')
end

.pseudogenic_tRNA ⇒ Object

A non functional descendent of a tRNA. (http://purl.obolibrary.org/obo/SO_0000778)

# File 'lib/biointerchange/so.rb', line 4985

def self.pseudogenic_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000778')
end

.pseudoknot ⇒ Object

A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop. (http://purl.obolibrary.org/obo/SO_0000591)

# File 'lib/biointerchange/so.rb', line 3869

def self.pseudoknot
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000591')
end

.pseudouridine ⇒ Object

A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position. (http://purl.obolibrary.org/obo/SO_0001229)

# File 'lib/biointerchange/so.rb', line 7645

def self.pseudouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001229')
end

.pseudouridylation_guide_snoRNA ⇒ Object

A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue. (http://purl.obolibrary.org/obo/SO_0001187)

# File 'lib/biointerchange/so.rb', line 7393

def self.pseudouridylation_guide_snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001187')
end

.purine_to_pyrimidine_transversion ⇒ Object

Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T. (http://purl.obolibrary.org/obo/SO_1000023)

# File 'lib/biointerchange/so.rb', line 12581

def self.purine_to_pyrimidine_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000023')
end

.purine_transition ⇒ Object

A substitution of a purine, A or G, for another purine. (http://purl.obolibrary.org/obo/SO_1000014)

# File 'lib/biointerchange/so.rb', line 12527

def self.purine_transition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000014')
end

.pyrimidine_to_purine_transversion ⇒ Object

Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G. (http://purl.obolibrary.org/obo/SO_1000018)

# File 'lib/biointerchange/so.rb', line 12551

def self.pyrimidine_to_purine_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000018')
end

.pyrimidine_transition ⇒ Object

A substitution of a pyrimidine, C or T, for another pyrimidine. (http://purl.obolibrary.org/obo/SO_1000010)

# File 'lib/biointerchange/so.rb', line 12503

def self.pyrimidine_transition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000010')
end

.pyrosequenced_read ⇒ Object

A read produced by pyrosequencing technology. (http://purl.obolibrary.org/obo/SO_0001424)

# File 'lib/biointerchange/so.rb', line 8809

def self.pyrosequenced_read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001424')
end

.pyrrolysine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001456)

# File 'lib/biointerchange/so.rb', line 8995

def self.pyrrolysine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001456')
end

.pyrrolysine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding pyrrolysyl tRNA (SO:0000766). (http://purl.obolibrary.org/obo/SO_0001178)

# File 'lib/biointerchange/so.rb', line 7339

def self.pyrrolysine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001178')
end

.pyrrolysyl_tRNA ⇒ Object

A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region. (http://purl.obolibrary.org/obo/SO_0000766)

# File 'lib/biointerchange/so.rb', line 4919

def self.pyrrolysyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000766')
end

.QTL ⇒ Object

A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. (http://purl.obolibrary.org/obo/SO_0000771)

# File 'lib/biointerchange/so.rb', line 4943

def self.QTL
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000771')
end

.quality_value ⇒ Object

An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score. (http://purl.obolibrary.org/obo/SO_0001686)

# File 'lib/biointerchange/so.rb', line 10327

def self.quality_value
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001686')
end

.quantitative_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001774)

# File 'lib/biointerchange/so.rb', line 10855

def self.quantitative_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001774')
end

.queuosine ⇒ Object

Queuosine is a modified 7-deazoguanosine. (http://purl.obolibrary.org/obo/SO_0001317)

# File 'lib/biointerchange/so.rb', line 8167

def self.queuosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001317')
end

.R_five_prime_LTR_region ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000427)

# File 'lib/biointerchange/so.rb', line 2877

def self.R_five_prime_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000427')
end

.R_GNA ⇒ Object

An attribute describing a GNA sequence in the (R)-GNA enantiomer. (http://purl.obolibrary.org/obo/SO_0001194)

# File 'lib/biointerchange/so.rb', line 7435

def self.R_GNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001194')
end

.R_GNA_oligo ⇒ Object

An oligo composed of (R)-GNA residues. (http://purl.obolibrary.org/obo/SO_0001195)

# File 'lib/biointerchange/so.rb', line 7441

def self.R_GNA_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001195')
end

.R_LTR_region ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000423)

# File 'lib/biointerchange/so.rb', line 2853

def self.R_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000423')
end

.R_three_prime_LTR_region ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000430)

# File 'lib/biointerchange/so.rb', line 2895

def self.R_three_prime_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000430')
end

.random_sequence ⇒ Object

A sequence of nucleotides or amino acids which, by design, has a "random" order of components, given a predetermined input frequency of these components. (SO:ma) (http://purl.obolibrary.org/obo/SO_0000449)

# File 'lib/biointerchange/so.rb', line 3013

def self.random_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000449')
end

.RAPD ⇒ Object

RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers. (http://purl.obolibrary.org/obo/SO_0001481)

# File 'lib/biointerchange/so.rb', line 9145

def self.RAPD
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001481')
end

.rare_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001765)

# File 'lib/biointerchange/so.rb', line 10801

def self.rare_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001765')
end

.rasiRNA ⇒ Object

A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements. (http://purl.obolibrary.org/obo/SO_0000454)

# File 'lib/biointerchange/so.rb', line 3043

def self.rasiRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000454')
end

.rate_of_transcription_variant ⇒ Object

A sequence variant that changes the rate of transcription with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001550)

# File 'lib/biointerchange/so.rb', line 9559

def self.rate_of_transcription_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001550')
end

.rDNA_intergenic_spacer_element ⇒ Object

A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1). (http://purl.obolibrary.org/obo/SO_0001860)

# File 'lib/biointerchange/so.rb', line 11365

def self.rDNA_intergenic_spacer_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001860')
end

.rDNA_replication_fork_barrier ⇒ Object

A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing. (http://purl.obolibrary.org/obo/SO_0001914)

# File 'lib/biointerchange/so.rb', line 11689

def self.rDNA_replication_fork_barrier
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001914')
end

.read ⇒ Object

A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine. (http://purl.obolibrary.org/obo/SO_0000150)

# File 'lib/biointerchange/so.rb', line 1217

def self.read
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000150')
end

.read_pair ⇒ Object

One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert. (http://purl.obolibrary.org/obo/SO_0000007)

# File 'lib/biointerchange/so.rb', line 357

def self.read_pair
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000007')
end

.reading_frame ⇒ Object

A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon. (http://purl.obolibrary.org/obo/SO_0000717)

# File 'lib/biointerchange/so.rb', line 4625

def self.reading_frame
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000717')
end

.reagent ⇒ Object

A sequence used in experiment. (http://purl.obolibrary.org/obo/SO_0000695)

# File 'lib/biointerchange/so.rb', line 4493

def self.reagent
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000695')
end

.reagent_attribute ⇒ Object

Added jan 2006 by KE. (http://purl.obolibrary.org/obo/SO_0000786)

# File 'lib/biointerchange/so.rb', line 5033

def self.reagent_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000786')
end

.rearranged_at_DNA_level ⇒ Object

An attribute to describe the sequence of a feature, where the DNA is rearranged. (http://purl.obolibrary.org/obo/SO_0000904)

# File 'lib/biointerchange/so.rb', line 5705

def self.rearranged_at_DNA_level
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000904')
end

.rearrangement_breakpoint ⇒ Object

A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome. (http://purl.obolibrary.org/obo/SO_0001872)

# File 'lib/biointerchange/so.rb', line 11437

def self.rearrangement_breakpoint
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001872')
end

.reciprocal ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001521)

# File 'lib/biointerchange/so.rb', line 9385

def self.reciprocal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001521')
end

.reciprocal_chromosomal_translocation ⇒ Object

A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged. (http://purl.obolibrary.org/obo/SO_1000048)

# File 'lib/biointerchange/so.rb', line 12719

def self.reciprocal_chromosomal_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000048')
end

.recoded ⇒ Object

An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations. (http://purl.obolibrary.org/obo/SO_0000881)

# File 'lib/biointerchange/so.rb', line 5567

def self.recoded
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000881')
end

.recoded_by_translational_bypass ⇒ Object

Recoded mRNA where a block of nucleotides is not translated. (http://purl.obolibrary.org/obo/SO_0000886)

# File 'lib/biointerchange/so.rb', line 5597

def self.recoded_by_translational_bypass
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000886')
end

.recoded_codon ⇒ Object

A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough. (http://purl.obolibrary.org/obo/SO_0000145)

# File 'lib/biointerchange/so.rb', line 1187

def self.recoded_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000145')
end

.recoded_mRNA ⇒ Object

The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals. (http://purl.obolibrary.org/obo/SO_1001261)

# File 'lib/biointerchange/so.rb', line 13511

def self.recoded_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001261')
end

.recoding_pseudoknot ⇒ Object

The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding. (http://purl.obolibrary.org/obo/SO_0000545)

# File 'lib/biointerchange/so.rb', line 3589

def self.recoding_pseudoknot
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000545')
end

.recoding_stimulatory_region ⇒ Object

A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA. (http://purl.obolibrary.org/obo/SO_1001268)

# File 'lib/biointerchange/so.rb', line 13553

def self.recoding_stimulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001268')
end

.recombination_feature ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000298)

# File 'lib/biointerchange/so.rb', line 2109

def self.recombination_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000298')
end

.recombination_feature_of_rearranged_gene ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000300)

# File 'lib/biointerchange/so.rb', line 2121

def self.recombination_feature_of_rearranged_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000300')
end

.recombination_hotspot ⇒ Object

A region in a genome which promotes recombination. (http://purl.obolibrary.org/obo/SO_0000339)

# File 'lib/biointerchange/so.rb', line 2355

def self.recombination_hotspot
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000339')
end

.recombination_regulatory_region ⇒ Object

A regulatory region that is involved in the control of the process of recombination. (http://purl.obolibrary.org/obo/SO_0001681)

# File 'lib/biointerchange/so.rb', line 10297

def self.recombination_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001681')
end

.recombination_signal_sequence ⇒ Object

A region recognized by a recombinase. (http://purl.obolibrary.org/obo/SO_0001532)

# File 'lib/biointerchange/so.rb', line 9451

def self.recombination_signal_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001532')
end

.recombinationally_inverted_gene ⇒ Object

A recombinationally rearranged gene by inversion. (http://purl.obolibrary.org/obo/SO_0000373)

# File 'lib/biointerchange/so.rb', line 2553

def self.recombinationally_inverted_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000373')
end

.recombinationally_rearranged ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000940)

# File 'lib/biointerchange/so.rb', line 5921

def self.recombinationally_rearranged
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000940')
end

.recombinationally_rearranged_gene ⇒ Object

A gene that is recombinationally rearranged. (http://purl.obolibrary.org/obo/SO_0000456)

# File 'lib/biointerchange/so.rb', line 3055

def self.recombinationally_rearranged_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000456')
end

.recombinationally_rearranged_vertebrate_immune_system_gene ⇒ Object

A recombinationally rearranged gene of the vertebrate immune system. (http://purl.obolibrary.org/obo/SO_0000941)

# File 'lib/biointerchange/so.rb', line 5927

def self.recombinationally_rearranged_vertebrate_immune_system_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000941')
end

.recombined_from ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#recombined_from)

# File 'lib/biointerchange/so.rb', line 233

def self.recombined_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#recombined_from')
end

.recombined_to ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#recombined_to)

# File 'lib/biointerchange/so.rb', line 239

def self.recombined_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#recombined_to')
end

.recursive_splice_site ⇒ Object

A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons. (http://purl.obolibrary.org/obo/SO_0000998)

# File 'lib/biointerchange/so.rb', line 6263

def self.recursive_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000998')
end

.reference_genome ⇒ Object

A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly. (http://purl.obolibrary.org/obo/SO_0001505)

# File 'lib/biointerchange/so.rb', line 9289

def self.reference_genome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001505')
end

.region ⇒ Object

A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. (http://purl.obolibrary.org/obo/SO_0000001)

# File 'lib/biointerchange/so.rb', line 321

def self.region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000001')
end

.regional_centromere ⇒ Object

A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions. (http://purl.obolibrary.org/obo/SO_0001795)

# File 'lib/biointerchange/so.rb', line 10975

def self.regional_centromere
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001795')
end

.regional_centromere_central_core ⇒ Object

A conserved region within the central region of a modular centromere, where the kinetochore is formed. (http://purl.obolibrary.org/obo/SO_0001796)

# File 'lib/biointerchange/so.rb', line 10981

def self.regional_centromere_central_core
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001796')
end

.regional_centromere_inner_repeat_region ⇒ Object

The inner inverted repeat region of a modular centromere and part of the entral core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm. (http://purl.obolibrary.org/obo/SO_0001798)

# File 'lib/biointerchange/so.rb', line 10993

def self.regional_centromere_inner_repeat_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001798')
end

.regional_centromere_outer_repeat_region ⇒ Object

The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms. (http://purl.obolibrary.org/obo/SO_0001799)

# File 'lib/biointerchange/so.rb', line 10999

def self.regional_centromere_outer_repeat_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001799')
end

.regional_centromere_outer_repeat_transcript ⇒ Object

A transcript that is transcribed from the outer repeat region of a regional centromere. (http://purl.obolibrary.org/obo/SO_0001905)

# File 'lib/biointerchange/so.rb', line 11635

def self.regional_centromere_outer_repeat_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001905')
end

.regulated ⇒ Object

An attribute to describe a sequence that is regulated. (http://purl.obolibrary.org/obo/SO_0000119)

# File 'lib/biointerchange/so.rb', line 1031

def self.regulated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000119')
end

.regulatory_promoter_element ⇒ Object

A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region. (http://purl.obolibrary.org/obo/SO_0001678)

# File 'lib/biointerchange/so.rb', line 10279

def self.regulatory_promoter_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001678')
end

.regulatory_region ⇒ Object

A region of sequence that is involved in the control of a biological process. (http://purl.obolibrary.org/obo/SO_0005836)

# File 'lib/biointerchange/so.rb', line 12251

def self.regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005836')
end

.regulatory_region_ablation ⇒ Object

A feature ablation whereby the deleted region includes a regulatory region. (http://purl.obolibrary.org/obo/SO_0001894)

# File 'lib/biointerchange/so.rb', line 11569

def self.regulatory_region_ablation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001894')
end

.regulatory_region_amplification ⇒ Object

A feature amplification of a region containing a regulatory region. (http://purl.obolibrary.org/obo/SO_0001891)

# File 'lib/biointerchange/so.rb', line 11551

def self.regulatory_region_amplification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001891')
end

.regulatory_region_fusion ⇒ Object

A feature fusion where the deletion brings together regulatory regions. (http://purl.obolibrary.org/obo/SO_0001887)

# File 'lib/biointerchange/so.rb', line 11527

def self.regulatory_region_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001887')
end

.regulatory_region_translocation ⇒ Object

A feature translocation where the region contains a regulatory region. (http://purl.obolibrary.org/obo/SO_0001884)

# File 'lib/biointerchange/so.rb', line 11509

def self.regulatory_region_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001884')
end

.regulatory_region_variant ⇒ Object

A sequence variant located within a regulatory region. (http://purl.obolibrary.org/obo/SO_0001566)

# File 'lib/biointerchange/so.rb', line 9655

def self.regulatory_region_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001566')
end

.regulon ⇒ Object

A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal. (http://purl.obolibrary.org/obo/SO_1001284)

# File 'lib/biointerchange/so.rb', line 13637

def self.regulon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001284')
end

.remark ⇒ Object

A comment about the sequence. (http://purl.obolibrary.org/obo/SO_0000700)

# File 'lib/biointerchange/so.rb', line 4523

def self.remark
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000700')
end

.repeat_component ⇒ Object

A region of a repeated sequence. (http://purl.obolibrary.org/obo/SO_0000840)

# File 'lib/biointerchange/so.rb', line 5321

def self.repeat_component
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000840')
end

.repeat_family ⇒ Object

A group of characterized repeat sequences. (http://purl.obolibrary.org/obo/SO_0000187)

# File 'lib/biointerchange/so.rb', line 1443

def self.repeat_family
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000187')
end

.repeat_fragment ⇒ Object

A portion of a repeat, interrupted by the insertion of another element. (http://purl.obolibrary.org/obo/SO_0001050)

# File 'lib/biointerchange/so.rb', line 6575

def self.repeat_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001050')
end

.repeat_region ⇒ Object

A region of sequence containing one or more repeat units. (http://purl.obolibrary.org/obo/SO_0000657)

# File 'lib/biointerchange/so.rb', line 4265

def self.repeat_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000657')
end

.repeat_unit ⇒ Object

The simplest repeated component of a repeat region. A single repeat. (http://purl.obolibrary.org/obo/SO_0000726)

# File 'lib/biointerchange/so.rb', line 4679

def self.repeat_unit
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000726')
end

.repetitive_element ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000292)

# File 'lib/biointerchange/so.rb', line 2073

def self.repetitive_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000292')
end

.replication_regulatory_region ⇒ Object

A regulatory region that is involved in the control of the process of nucleotide replication. (http://purl.obolibrary.org/obo/SO_0001682)

# File 'lib/biointerchange/so.rb', line 10303

def self.replication_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001682')
end

.replicon ⇒ Object

A region containing at least one unique origin of replication and a unique termination site. (http://purl.obolibrary.org/obo/SO_0001235)

# File 'lib/biointerchange/so.rb', line 7681

def self.replicon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001235')
end

.rescue ⇒ Object

An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype. (http://purl.obolibrary.org/obo/SO_0000814)

# File 'lib/biointerchange/so.rb', line 5177

def self.rescue
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000814')
end

.rescue_gene ⇒ Object

A gene that rescues. (http://purl.obolibrary.org/obo/SO_0000816)

# File 'lib/biointerchange/so.rb', line 5189

def self.rescue_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000816')
end

.rescue_mini_gene ⇒ Object

A mini_gene that rescues. (http://purl.obolibrary.org/obo/SO_0000795)

# File 'lib/biointerchange/so.rb', line 5087

def self.rescue_mini_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000795')
end

.rescue_region ⇒ Object

A region that rescues. (http://purl.obolibrary.org/obo/SO_0000411)

# File 'lib/biointerchange/so.rb', line 2781

def self.rescue_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000411')
end

.resolution_site ⇒ Object

A region specifically recognised by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles. (http://purl.obolibrary.org/obo/SO_0000947)

# File 'lib/biointerchange/so.rb', line 5963

def self.resolution_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000947')
end

.restriction_enzyme_assembly_scar ⇒ Object

A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends. (http://purl.obolibrary.org/obo/SO_0001953)

# File 'lib/biointerchange/so.rb', line 11923

def self.restriction_enzyme_assembly_scar
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001953')
end

.restriction_enzyme_binding_site ⇒ Object

A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme. (http://purl.obolibrary.org/obo/SO_0000061)

# File 'lib/biointerchange/so.rb', line 683

def self.restriction_enzyme_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000061')
end

.restriction_enzyme_cleavage_junction ⇒ Object

The boundary at which a restriction enzyme breaks the nucleotide sequence. (http://purl.obolibrary.org/obo/SO_0001688)

# File 'lib/biointerchange/so.rb', line 10339

def self.restriction_enzyme_cleavage_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001688')
end

.restriction_enzyme_cut_site ⇒ Object

A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA. (http://purl.obolibrary.org/obo/SO_0000168)

# File 'lib/biointerchange/so.rb', line 1325

def self.restriction_enzyme_cut_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000168')
end

.restriction_enzyme_five_prime_single_strand_overhang ⇒ Object

A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end. (http://purl.obolibrary.org/obo/SO_0001932)

# File 'lib/biointerchange/so.rb', line 11797

def self.restriction_enzyme_five_prime_single_strand_overhang
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001932')
end

.restriction_enzyme_recognition_site ⇒ Object

The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site. (http://purl.obolibrary.org/obo/SO_0001687)

# File 'lib/biointerchange/so.rb', line 10333

def self.restriction_enzyme_recognition_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001687')
end

.restriction_enzyme_region ⇒ Object

A region related to restriction enzyme function. (http://purl.obolibrary.org/obo/SO_0001954)

# File 'lib/biointerchange/so.rb', line 11929

def self.restriction_enzyme_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001954')
end

.restriction_enzyme_single_strand_overhang ⇒ Object

A terminal region of DNA sequence where the end of the region is not blunt ended. (http://purl.obolibrary.org/obo/SO_0001695)

# File 'lib/biointerchange/so.rb', line 10381

def self.restriction_enzyme_single_strand_overhang
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001695')
end

.restriction_enzyme_three_prime_single_strand_overhang ⇒ Object

A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end. (http://purl.obolibrary.org/obo/SO_0001933)

# File 'lib/biointerchange/so.rb', line 11803

def self.restriction_enzyme_three_prime_single_strand_overhang
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001933')
end

.restriction_fragment ⇒ Object

A region of polynucleotide sequence produced by digestion with a restriction endonuclease. (http://purl.obolibrary.org/obo/SO_0000412)

# File 'lib/biointerchange/so.rb', line 2787

def self.restriction_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000412')
end

.retinoic_acid_responsive_element ⇒ Object

A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind. (http://purl.obolibrary.org/obo/SO_0001653)

# File 'lib/biointerchange/so.rb', line 10129

def self.retinoic_acid_responsive_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001653')
end

.retrogene ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001219)

# File 'lib/biointerchange/so.rb', line 7585

def self.retrogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001219')
end

.retron ⇒ Object

Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes. (http://purl.obolibrary.org/obo/SO_1001275)

# File 'lib/biointerchange/so.rb', line 13595

def self.retron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001275')
end

.retrotransposed ⇒ Object

An attribute of a feature that occurred as the product of a reverse transcriptase mediated event. (http://purl.obolibrary.org/obo/SO_0000569)

# File 'lib/biointerchange/so.rb', line 3737

def self.retrotransposed
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000569')
end

.retrotransposon ⇒ Object

A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase. (http://purl.obolibrary.org/obo/SO_0000180)

# File 'lib/biointerchange/so.rb', line 1401

def self.retrotransposon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000180')
end

.reverse ⇒ Object

Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer. (http://purl.obolibrary.org/obo/SO_0001031)

# File 'lib/biointerchange/so.rb', line 6461

def self.reverse
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001031')
end

.reverse_Hoogsteen_base_pair ⇒ Object

A type of non-canonical base-pairing. (http://purl.obolibrary.org/obo/SO_0000501)

# File 'lib/biointerchange/so.rb', line 3325

def self.reverse_Hoogsteen_base_pair
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000501')
end

.reverse_primer ⇒ Object

A single stranded oligo used for polymerase chain reaction. (http://purl.obolibrary.org/obo/SO_0000132)

# File 'lib/biointerchange/so.rb', line 1109

def self.reverse_primer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000132')
end

.RFLP_fragment ⇒ Object

A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme. (http://purl.obolibrary.org/obo/SO_0000193)

# File 'lib/biointerchange/so.rb', line 1479

def self.RFLP_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000193')
end

.RH_map ⇒ Object

A radiation hybrid map is a physical map. (http://purl.obolibrary.org/obo/SO_0001252)

# File 'lib/biointerchange/so.rb', line 7777

def self.RH_map
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001252')
end

.rho_dependent_bacterial_terminator ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000981)

# File 'lib/biointerchange/so.rb', line 6161

def self.rho_dependent_bacterial_terminator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000981')
end

.rho_independent_bacterial_terminator ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000982)

# File 'lib/biointerchange/so.rb', line 6167

def self.rho_independent_bacterial_terminator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000982')
end

.ribonuclease_site ⇒ Object

A region of a transcript encoding the cleavage site for a ribonuclease enzyme. (http://purl.obolibrary.org/obo/SO_0001977)

# File 'lib/biointerchange/so.rb', line 12071

def self.ribonuclease_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001977')
end

.ribosome_entry_site ⇒ Object

Region in mRNA where ribosome assembles. (http://purl.obolibrary.org/obo/SO_0000139)

# File 'lib/biointerchange/so.rb', line 1151

def self.ribosome_entry_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000139')
end

.riboswitch ⇒ Object

A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites. (http://purl.obolibrary.org/obo/SO_0000035)

# File 'lib/biointerchange/so.rb', line 519

def self.riboswitch
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000035')
end

.ribothymidine ⇒ Object

A modified RNA base in which thymine is bound to the ribose ring. (http://purl.obolibrary.org/obo/SO_0001232)

# File 'lib/biointerchange/so.rb', line 7663

def self.ribothymidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001232')
end

.ribozyme ⇒ Object

An RNA with catalytic activity. (http://purl.obolibrary.org/obo/SO_0000374)

# File 'lib/biointerchange/so.rb', line 2559

def self.ribozyme
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000374')
end

.ribozymic ⇒ Object

An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein. (http://purl.obolibrary.org/obo/SO_0001186)

# File 'lib/biointerchange/so.rb', line 7387

def self.ribozymic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001186')
end

.right_handed_peptide_helix ⇒ Object

A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw. (http://purl.obolibrary.org/obo/SO_0001116)

# File 'lib/biointerchange/so.rb', line 6967

def self.right_handed_peptide_helix
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001116')
end

.ring_chromosome ⇒ Object

A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome. (http://purl.obolibrary.org/obo/SO_1000045)

# File 'lib/biointerchange/so.rb', line 12701

def self.ring_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000045')
end

.RNA ⇒ Object

An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone. (http://purl.obolibrary.org/obo/SO_0000356)

# File 'lib/biointerchange/so.rb', line 2457

def self.RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000356')
end

.RNA_6S ⇒ Object

A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase. (http://purl.obolibrary.org/obo/SO_0000376)

# File 'lib/biointerchange/so.rb', line 2571

def self.RNA_6S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000376')
end

.RNA_aptamer ⇒ Object

RNA molecules that have been selected from random pools based on their ability to bind other molecules. (http://purl.obolibrary.org/obo/SO_0000033)

# File 'lib/biointerchange/so.rb', line 507

def self.RNA_aptamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000033')
end

.RNA_chromosome ⇒ Object

Structural unit composed of a self-replicating, RNA molecule. (http://purl.obolibrary.org/obo/SO_0000961)

# File 'lib/biointerchange/so.rb', line 6047

def self.RNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000961')
end

.RNA_hook_turn ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000027)

# File 'lib/biointerchange/so.rb', line 471

def self.RNA_hook_turn
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000027')
end

.RNA_internal_loop ⇒ Object

A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge. (http://purl.obolibrary.org/obo/SO_0000020)

# File 'lib/biointerchange/so.rb', line 429

def self.RNA_internal_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000020')
end

.RNA_junction_loop ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000026)

# File 'lib/biointerchange/so.rb', line 465

def self.RNA_junction_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000026')
end

.RNA_motif ⇒ Object

A motif that is active in RNA sequence. (http://purl.obolibrary.org/obo/SO_0000715)

# File 'lib/biointerchange/so.rb', line 4613

def self.RNA_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000715')
end

.RNA_polymerase_II_TATA_box ⇒ Object

A TATA box core promoter of a gene transcribed by RNA polymerase II. (http://purl.obolibrary.org/obo/SO_0001661)

# File 'lib/biointerchange/so.rb', line 10177

def self.RNA_polymerase_II_TATA_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001661')
end

.RNA_polymerase_III_TATA_box ⇒ Object

A TATA box core promoter of a gene transcribed by RNA polymerase III. (http://purl.obolibrary.org/obo/SO_0001662)

# File 'lib/biointerchange/so.rb', line 10183

def self.RNA_polymerase_III_TATA_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001662')
end

.RNA_polymerase_promoter ⇒ Object

A region (DNA) to which RNA polymerase binds, to begin transcription. (http://purl.obolibrary.org/obo/SO_0001203)

# File 'lib/biointerchange/so.rb', line 7489

def self.RNA_polymerase_promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001203')
end

.RNA_replication_mode ⇒ Object

This has been obsoleted as it represents a process. replaced_by: GO:0034961. (http://purl.obolibrary.org/obo/SO_0000972)

# File 'lib/biointerchange/so.rb', line 6113

def self.RNA_replication_mode
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000972')
end

.RNA_sequence_secondary_structure ⇒ Object

A folded RNA sequence. (http://purl.obolibrary.org/obo/SO_0000122)

# File 'lib/biointerchange/so.rb', line 1049

def self.RNA_sequence_secondary_structure
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000122')
end

.RNA_stability_element ⇒ Object

Either:

RNA secondary structure that affects the stability of an RNA molecule.
(http://purl.obolibrary.org/obo/SO_0001957)

Or:

A motif that affects the stability of RNA.
(http://purl.obolibrary.org/obo/SO_0001979)

# File 'lib/biointerchange/so.rb', line 11951

def self.RNA_stability_element
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001957'), RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001979') ]
end

.RNAi_reagent ⇒ Object

A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference. (http://purl.obolibrary.org/obo/SO_0000337)

# File 'lib/biointerchange/so.rb', line 2343

def self.RNAi_reagent
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000337')
end

.RNApol_I_promoter ⇒ Object

A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription. (http://purl.obolibrary.org/obo/SO_0000169)

# File 'lib/biointerchange/so.rb', line 1331

def self.RNApol_I_promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000169')
end

.RNApol_II_core_promoter ⇒ Object

The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes. (http://purl.obolibrary.org/obo/SO_0001669)

# File 'lib/biointerchange/so.rb', line 10225

def self.RNApol_II_core_promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001669')
end

.RNApol_II_promoter ⇒ Object

A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription. (http://purl.obolibrary.org/obo/SO_0000170)

# File 'lib/biointerchange/so.rb', line 1337

def self.RNApol_II_promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000170')
end

.RNApol_II_promoter_region ⇒ Object

A region of sequence which is a promoter for RNA polymerase II. (http://purl.obolibrary.org/obo/SO_0000844)

# File 'lib/biointerchange/so.rb', line 5345

def self.RNApol_II_promoter_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000844')
end

.RNApol_III_promoter ⇒ Object

A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription. (http://purl.obolibrary.org/obo/SO_0000171)

# File 'lib/biointerchange/so.rb', line 1343

def self.RNApol_III_promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000171')
end

.RNApol_III_promoter_type_1 ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000617)

# File 'lib/biointerchange/so.rb', line 4025

def self.RNApol_III_promoter_type_1
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000617')
end

.RNApol_III_promoter_type_1_region ⇒ Object

A region of sequence which is a promoter for RNA polymerase III type 1. (http://purl.obolibrary.org/obo/SO_0000845)

# File 'lib/biointerchange/so.rb', line 5351

def self.RNApol_III_promoter_type_1_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000845')
end

.RNApol_III_promoter_type_2 ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000618)

# File 'lib/biointerchange/so.rb', line 4031

def self.RNApol_III_promoter_type_2
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000618')
end

.RNApol_III_promoter_type_2_region ⇒ Object

A region of sequence which is a promoter for RNA polymerase III type 2. (http://purl.obolibrary.org/obo/SO_0000846)

# File 'lib/biointerchange/so.rb', line 5357

def self.RNApol_III_promoter_type_2_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000846')
end

.RNApol_III_promoter_type_3 ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000621)

# File 'lib/biointerchange/so.rb', line 4049

def self.RNApol_III_promoter_type_3
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000621')
end

.RNase_MRP_RNA ⇒ Object

The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs. (http://purl.obolibrary.org/obo/SO_0000385)

# File 'lib/biointerchange/so.rb', line 2625

def self.RNase_MRP_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000385')
end

.RNase_MRP_RNA_gene ⇒ Object

A gene that encodes a RNase_MRP_RNA. (http://purl.obolibrary.org/obo/SO_0001640)

# File 'lib/biointerchange/so.rb', line 10075

def self.RNase_MRP_RNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001640')
end

.RNase_P_RNA ⇒ Object

The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs. (http://purl.obolibrary.org/obo/SO_0000386)

# File 'lib/biointerchange/so.rb', line 2631

def self.RNase_P_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000386')
end

.RNase_P_RNA_gene ⇒ Object

A gene that encodes an RNase P RNA. (http://purl.obolibrary.org/obo/SO_0001639)

# File 'lib/biointerchange/so.rb', line 10069

def self.RNase_P_RNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001639')
end

.Robertsonian_fusion ⇒ Object

A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere. (http://purl.obolibrary.org/obo/SO_1000043)

# File 'lib/biointerchange/so.rb', line 12689

def self.Robertsonian_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000043')
end

.rolling_circle ⇒ Object

This has been obsoleted as it represents a process. replaced_by: GO:0070581. (http://purl.obolibrary.org/obo/SO_0000969)

# File 'lib/biointerchange/so.rb', line 6095

def self.rolling_circle
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000969')
end

.RprA_RNA ⇒ Object

Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential. (http://purl.obolibrary.org/obo/SO_0000387)

# File 'lib/biointerchange/so.rb', line 2637

def self.RprA_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000387')
end

.RR_tract ⇒ Object

A polypurine tract within an LTR_retrotransposon. (http://purl.obolibrary.org/obo/SO_0000435)

# File 'lib/biointerchange/so.rb', line 2925

def self.RR_tract
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000435')
end

.RRE_RNA ⇒ Object

The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins. (http://purl.obolibrary.org/obo/SO_0000388)

# File 'lib/biointerchange/so.rb', line 2643

def self.RRE_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000388')
end

.rRNA ⇒ Object

RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity. (http://purl.obolibrary.org/obo/SO_0000252)

# File 'lib/biointerchange/so.rb', line 1833

def self.rRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000252')
end

.rRNA_16S ⇒ Object

A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome. (http://purl.obolibrary.org/obo/SO_0001000)

# File 'lib/biointerchange/so.rb', line 6275

def self.rRNA_16S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001000')
end

.rRNA_18S ⇒ Object

A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome. (http://purl.obolibrary.org/obo/SO_0000407)

# File 'lib/biointerchange/so.rb', line 2757

def self.rRNA_18S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000407')
end

.rRNA_21S ⇒ Object

A component of the large ribosomal subunit in mitochondrial rRNA. (http://purl.obolibrary.org/obo/SO_0001171)

# File 'lib/biointerchange/so.rb', line 7297

def self.rRNA_21S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001171')
end

.rRNA_23S ⇒ Object

A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome. (http://purl.obolibrary.org/obo/SO_0001001)

# File 'lib/biointerchange/so.rb', line 6281

def self.rRNA_23S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001001')
end

.rRNA_25S ⇒ Object

A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes. (http://purl.obolibrary.org/obo/SO_0001002)

# File 'lib/biointerchange/so.rb', line 6287

def self.rRNA_25S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001002')
end

.rRNA_28S ⇒ Object

A component of the large ribosomal subunit. (http://purl.obolibrary.org/obo/SO_0000653)

# File 'lib/biointerchange/so.rb', line 4241

def self.rRNA_28S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000653')
end

.rRNA_5_8S ⇒ Object

5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea. (http://purl.obolibrary.org/obo/SO_0000375)

# File 'lib/biointerchange/so.rb', line 2565

def self.rRNA_5_8S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000375')
end

.rRNA_5S ⇒ Object

5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription. (http://purl.obolibrary.org/obo/SO_0000652)

# File 'lib/biointerchange/so.rb', line 4235

def self.rRNA_5S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000652')
end

.rRNA_cleavage_RNA ⇒ Object

An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules. (http://purl.obolibrary.org/obo/SO_0005843)

# File 'lib/biointerchange/so.rb', line 12269

def self.rRNA_cleavage_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005843')
end

.rRNA_cleavage_snoRNA_primary_transcript ⇒ Object

A primary transcript encoding an rRNA cleavage snoRNA. (http://purl.obolibrary.org/obo/SO_0000582)

# File 'lib/biointerchange/so.rb', line 3815

def self.rRNA_cleavage_snoRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000582')
end

.rRNA_encoding ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000573)

# File 'lib/biointerchange/so.rb', line 3761

def self.rRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000573')
end

.rRNA_gene ⇒ Object

A gene that encodes for ribosomal RNA. (http://purl.obolibrary.org/obo/SO_0001637)

# File 'lib/biointerchange/so.rb', line 10057

def self.rRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001637')
end

.rRNA_large_subunit_primary_transcript ⇒ Object

A primary transcript encoding a large ribosomal subunit RNA. (http://purl.obolibrary.org/obo/SO_0000325)

# File 'lib/biointerchange/so.rb', line 2271

def self.rRNA_large_subunit_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000325')
end

.rRNA_primary_transcript ⇒ Object

A primary transcript encoding a ribosomal RNA. (http://purl.obolibrary.org/obo/SO_0000209)

# File 'lib/biointerchange/so.rb', line 1575

def self.rRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000209')
end

.rRNA_primary_transcript_region ⇒ Object

A region of an rRNA primary transcript. (http://purl.obolibrary.org/obo/SO_0000838)

# File 'lib/biointerchange/so.rb', line 5309

def self.rRNA_primary_transcript_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000838')
end

.rRNA_small_subunit_primary_transcript ⇒ Object

A primary transcript encoding a small ribosomal subunit RNA. (http://purl.obolibrary.org/obo/SO_0000255)

# File 'lib/biointerchange/so.rb', line 1851

def self.rRNA_small_subunit_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000255')
end

.RST ⇒ Object

A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long. (http://purl.obolibrary.org/obo/SO_0001467)

# File 'lib/biointerchange/so.rb', line 9061

def self.RST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001467')
end

.RST_match ⇒ Object

A match against an RST sequence. (http://purl.obolibrary.org/obo/SO_0001471)

# File 'lib/biointerchange/so.rb', line 9085

def self.RST_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001471')
end

.S_GNA ⇒ Object

An attribute describing a GNA sequence in the (S)-GNA enantiomer. (http://purl.obolibrary.org/obo/SO_0001196)

# File 'lib/biointerchange/so.rb', line 7447

def self.S_GNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001196')
end

.S_GNA_oligo ⇒ Object

An oligo composed of (S)-GNA residues. (http://purl.obolibrary.org/obo/SO_0001197)

# File 'lib/biointerchange/so.rb', line 7453

def self.S_GNA_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001197')
end

.S_region ⇒ Object

The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell. (http://purl.obolibrary.org/obo/SO_0001836)

# File 'lib/biointerchange/so.rb', line 11221

def self.S_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001836')
end

.SAGE_tag ⇒ Object

A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts. (http://purl.obolibrary.org/obo/SO_0000326)

# File 'lib/biointerchange/so.rb', line 2277

def self.SAGE_tag
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000326')
end

.Sap1_recognition_motif ⇒ Object

A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats. (http://purl.obolibrary.org/obo/SO_0001864)

# File 'lib/biointerchange/so.rb', line 11389

def self.Sap1_recognition_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001864')
end

.sarcin_like_RNA_motif ⇒ Object

A loop in ribosomal RNA containing the sites of attack for ricin and sarcin. (http://purl.obolibrary.org/obo/SO_0000024)

# File 'lib/biointerchange/so.rb', line 453

def self.sarcin_like_RNA_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000024')
end

.satellite_DNA ⇒ Object

The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA. (http://purl.obolibrary.org/obo/SO_0000005)

# File 'lib/biointerchange/so.rb', line 345

def self.satellite_DNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000005')
end

.schellmann_loop ⇒ Object

A motif of six or seven consecutive residues that contains two H-bonds. (http://purl.obolibrary.org/obo/SO_0001123)

# File 'lib/biointerchange/so.rb', line 7009

def self.schellmann_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001123')
end

.schellmann_loop_seven ⇒ Object

Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5). (http://purl.obolibrary.org/obo/SO_0001124)

# File 'lib/biointerchange/so.rb', line 7015

def self.schellmann_loop_seven
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001124')
end

.schellmann_loop_six ⇒ Object

Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4). (http://purl.obolibrary.org/obo/SO_0001125)

# File 'lib/biointerchange/so.rb', line 7021

def self.schellmann_loop_six
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001125')
end

.score ⇒ Object

The score of an experimentally derived feature such as a p-value. (http://purl.obolibrary.org/obo/SO_0001685)

# File 'lib/biointerchange/so.rb', line 10321

def self.score
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001685')
end

.scRNA ⇒ Object

A small non coding RNA sequence, present in the cytoplasm. (http://purl.obolibrary.org/obo/SO_0000013)

# File 'lib/biointerchange/so.rb', line 393

def self.scRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000013')
end

.scRNA_encoding ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000575)

# File 'lib/biointerchange/so.rb', line 3773

def self.scRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000575')
end

.scRNA_gene ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001266)

# File 'lib/biointerchange/so.rb', line 7861

def self.scRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001266')
end

.scRNA_primary_transcript ⇒ Object

The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote. (http://purl.obolibrary.org/obo/SO_0000012)

# File 'lib/biointerchange/so.rb', line 387

def self.scRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000012')
end

.SECIS_element ⇒ Object

The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes. (http://purl.obolibrary.org/obo/SO_1001274)

# File 'lib/biointerchange/so.rb', line 13589

def self.SECIS_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001274')
end

.selenocysteine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001455)

# File 'lib/biointerchange/so.rb', line 8989

def self.selenocysteine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001455')
end

.selenocysteine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding seryl tRNA (SO:000269). (http://purl.obolibrary.org/obo/SO_0005856)

# File 'lib/biointerchange/so.rb', line 12335

def self.selenocysteine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005856')
end

.selenocysteinyl_tRNA ⇒ Object

A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region. (http://purl.obolibrary.org/obo/SO_0005857)

# File 'lib/biointerchange/so.rb', line 12341

def self.selenocysteinyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005857')
end

.sequence_alteration ⇒ Object

A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. (http://purl.obolibrary.org/obo/SO_0001059)

# File 'lib/biointerchange/so.rb', line 6637

def self.sequence_alteration
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001059')
end

.sequence_assembly ⇒ Object

A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. (http://purl.obolibrary.org/obo/SO_0000353)

# File 'lib/biointerchange/so.rb', line 2439

def self.sequence_assembly
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000353')
end

.sequence_attribute ⇒ Object

An attribute describes a quality of sequence. (http://purl.obolibrary.org/obo/SO_0000400)

# File 'lib/biointerchange/so.rb', line 2715

def self.sequence_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000400')
end

.sequence_collection ⇒ Object

A collection of discontinuous sequences. (http://purl.obolibrary.org/obo/SO_0001260)

# File 'lib/biointerchange/so.rb', line 7825

def self.sequence_collection
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001260')
end

.sequence_conflict ⇒ Object

Different sources report differing sequences. (http://purl.obolibrary.org/obo/SO_0001085)

# File 'lib/biointerchange/so.rb', line 6781

def self.sequence_conflict
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001085')
end

.sequence_difference ⇒ Object

A region where the sequence differs from that of a specified sequence. (http://purl.obolibrary.org/obo/SO_0000413)

# File 'lib/biointerchange/so.rb', line 2793

def self.sequence_difference
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000413')
end

.sequence_feature ⇒ Object

Any extent of continuous biological sequence. (http://purl.obolibrary.org/obo/SO_0000110)

# File 'lib/biointerchange/so.rb', line 977

def self.sequence_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000110')
end

.sequence_feature_locating_method ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000308)

# File 'lib/biointerchange/so.rb', line 2169

def self.sequence_feature_locating_method
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000308')
end

.sequence_length_variation ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000248)

# File 'lib/biointerchange/so.rb', line 1809

def self.sequence_length_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000248')
end

.sequence_location ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000735)

# File 'lib/biointerchange/so.rb', line 4733

def self.sequence_location
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000735')
end

.sequence_motif ⇒ Object

A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance. (http://purl.obolibrary.org/obo/SO_0001683)

# File 'lib/biointerchange/so.rb', line 10309

def self.sequence_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001683')
end

.sequence_of ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#sequence_of)

# File 'lib/biointerchange/so.rb', line 245

def self.sequence_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#sequence_of')
end

.Sequence_Ontology ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000000)

# File 'lib/biointerchange/so.rb', line 315

def self.Sequence_Ontology
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000000')
end

.sequence_operation ⇒ Object

An operation that can be applied to a sequence, that results in a change. (http://purl.obolibrary.org/obo/SO_0000041)

# File 'lib/biointerchange/so.rb', line 555

def self.sequence_operation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000041')
end

.sequence_rearrangement_feature ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000669)

# File 'lib/biointerchange/so.rb', line 4337

def self.sequence_rearrangement_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000669')
end

.sequence_replication_mode ⇒ Object

This has been obsoleted as it represents a process. replaced_by: GO:0034961. (http://purl.obolibrary.org/obo/SO_0000968)

# File 'lib/biointerchange/so.rb', line 6089

def self.sequence_replication_mode
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000968')
end

.sequence_secondary_structure ⇒ Object

A folded sequence. (http://purl.obolibrary.org/obo/SO_0000002)

# File 'lib/biointerchange/so.rb', line 327

def self.sequence_secondary_structure
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000002')
end

.sequence_uncertainty ⇒ Object

Describes the positions in a sequence where the authors are unsure about the sequence assignment. (http://purl.obolibrary.org/obo/SO_0001086)

# File 'lib/biointerchange/so.rb', line 6787

def self.sequence_uncertainty
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001086')
end

.sequence_variant ⇒ Object

A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. (http://purl.obolibrary.org/obo/SO_0001060)

# File 'lib/biointerchange/so.rb', line 6643

def self.sequence_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001060')
end

.sequence_variant_affecting_3D_structure_of_polypeptide ⇒ Object

A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule. (http://purl.obolibrary.org/obo/SO_1000111)

# File 'lib/biointerchange/so.rb', line 13061

def self.sequence_variant_affecting_3D_structure_of_polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000111')
end

.sequence_variant_affecting_copy_number ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_0001020)

# File 'lib/biointerchange/so.rb', line 6395

def self.sequence_variant_affecting_copy_number
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001020')
end

.sequence_variant_affecting_editing ⇒ Object

Sequence variant affects the editing of the transcript. (http://purl.obolibrary.org/obo/SO_1000075)

# File 'lib/biointerchange/so.rb', line 12863

def self.sequence_variant_affecting_editing
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000075')
end

.sequence_variant_affecting_gene_structure ⇒ Object

A sequence_variant_effect that changes the gene structure. (http://purl.obolibrary.org/obo/SO_1000180)

# File 'lib/biointerchange/so.rb', line 13337

def self.sequence_variant_affecting_gene_structure
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000180')
end

.sequence_variant_affecting_level_of_translational_product ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000102)

# File 'lib/biointerchange/so.rb', line 13007

def self.sequence_variant_affecting_level_of_translational_product
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000102')
end

.sequence_variant_affecting_polyadenylation ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_0001432)

# File 'lib/biointerchange/so.rb', line 8851

def self.sequence_variant_affecting_polyadenylation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001432')
end

.sequence_variant_affecting_polypeptide_amino_acid_sequence ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000105)

# File 'lib/biointerchange/so.rb', line 13025

def self.sequence_variant_affecting_polypeptide_amino_acid_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000105')
end

.sequence_variant_affecting_polypeptide_function ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000117)

# File 'lib/biointerchange/so.rb', line 13085

def self.sequence_variant_affecting_polypeptide_function
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000117')
end

.sequence_variant_affecting_rate_of_transcription ⇒ Object

A mutation that alters the rate a which transcription of the sequence occurs. (http://purl.obolibrary.org/obo/SO_1000081)

# File 'lib/biointerchange/so.rb', line 12893

def self.sequence_variant_affecting_rate_of_transcription
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000081')
end

.sequence_variant_affecting_regulatory_region ⇒ Object

A sequence_variant_effect which changes the regulatory region of a gene. (http://purl.obolibrary.org/obo/SO_0000053)

# File 'lib/biointerchange/so.rb', line 631

def self.sequence_variant_affecting_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000053')
end

.sequence_variant_affecting_splice_acceptor ⇒ Object

A sequence_variant_effect that changes the splice acceptor sequence. (http://purl.obolibrary.org/obo/SO_1000073)

# File 'lib/biointerchange/so.rb', line 12851

def self.sequence_variant_affecting_splice_acceptor
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000073')
end

.sequence_variant_affecting_splice_donor ⇒ Object

A sequence_variant_effect that changes the splice donor sequence. (http://purl.obolibrary.org/obo/SO_1000072)

# File 'lib/biointerchange/so.rb', line 12845

def self.sequence_variant_affecting_splice_donor
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000072')
end

.sequence_variant_affecting_splicing ⇒ Object

A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed. (http://purl.obolibrary.org/obo/SO_1000071)

# File 'lib/biointerchange/so.rb', line 12839

def self.sequence_variant_affecting_splicing
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000071')
end

.sequence_variant_affecting_transcript_processing ⇒ Object

Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript. (http://purl.obolibrary.org/obo/SO_1000070)

# File 'lib/biointerchange/so.rb', line 12833

def self.sequence_variant_affecting_transcript_processing
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000070')
end

.sequence_variant_affecting_transcript_secondary_structure ⇒ Object

A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule. (http://purl.obolibrary.org/obo/SO_1000126)

# File 'lib/biointerchange/so.rb', line 13139

def self.sequence_variant_affecting_transcript_secondary_structure
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000126')
end

.sequence_variant_affecting_transcript_stability ⇒ Object

Sequence variant affects the stability of the transcript. (http://purl.obolibrary.org/obo/SO_1000082)

# File 'lib/biointerchange/so.rb', line 12899

def self.sequence_variant_affecting_transcript_stability
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000082')
end

.sequence_variant_affecting_transcription ⇒ Object

Mutation affects the process of transcription, its initiation, progression or termination. (http://purl.obolibrary.org/obo/SO_1000076)

# File 'lib/biointerchange/so.rb', line 12869

def self.sequence_variant_affecting_transcription
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000076')
end

.sequence_variant_affecting_translational_product ⇒ Object

A sequence variant causing a change in primary translation product of a transcript. (http://purl.obolibrary.org/obo/SO_1000088)

# File 'lib/biointerchange/so.rb', line 12935

def self.sequence_variant_affecting_translational_product
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000088')
end

.sequence_variant_causes_exon_loss ⇒ Object

A sequence variant affecting splicing and causes an exon loss. (http://purl.obolibrary.org/obo/SO_1000184)

# File 'lib/biointerchange/so.rb', line 13361

def self.sequence_variant_causes_exon_loss
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000184')
end

.sequence_variant_causes_intron_gain ⇒ Object

A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072). (http://purl.obolibrary.org/obo/SO_1000185)

# File 'lib/biointerchange/so.rb', line 13367

def self.sequence_variant_causes_intron_gain
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000185')
end

.sequence_variant_causing_amino_acid_coding_codon_change_in_transcript ⇒ Object

The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons. (http://purl.obolibrary.org/obo/SO_1000056)

# File 'lib/biointerchange/so.rb', line 12749

def self.sequence_variant_causing_amino_acid_coding_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000056')
end

.sequence_variant_causing_amino_acid_deletion ⇒ Object

The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence. (http://purl.obolibrary.org/obo/SO_1000097)

# File 'lib/biointerchange/so.rb', line 12977

def self.sequence_variant_causing_amino_acid_deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000097')
end

.sequence_variant_causing_amino_acid_insertion ⇒ Object

The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence. (http://purl.obolibrary.org/obo/SO_1000096)

# File 'lib/biointerchange/so.rb', line 12971

def self.sequence_variant_causing_amino_acid_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000096')
end

.sequence_variant_causing_amino_acid_substitution ⇒ Object

The replacement of a single amino acid by another. (http://purl.obolibrary.org/obo/SO_1000093)

# File 'lib/biointerchange/so.rb', line 12953

def self.sequence_variant_causing_amino_acid_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000093')
end

.sequence_variant_causing_compensatory_transcript_secondary_structure_mutation ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000127)

# File 'lib/biointerchange/so.rb', line 13145

def self.sequence_variant_causing_compensatory_transcript_secondary_structure_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000127')
end

.sequence_variant_causing_complex_3D_structural_change ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000115)

# File 'lib/biointerchange/so.rb', line 13073

def self.sequence_variant_causing_complex_3D_structural_change
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000115')
end

.sequence_variant_causing_complex_change_of_translational_product ⇒ Object

Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms. (http://purl.obolibrary.org/obo/SO_1000092)

# File 'lib/biointerchange/so.rb', line 12947

def self.sequence_variant_causing_complex_change_of_translational_product
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000092')
end

.sequence_variant_causing_conformational_change ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000116)

# File 'lib/biointerchange/so.rb', line 13079

def self.sequence_variant_causing_conformational_change
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000116')
end

.sequence_variant_causing_conservative_amino_acid_substitution ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000094)

# File 'lib/biointerchange/so.rb', line 12959

def self.sequence_variant_causing_conservative_amino_acid_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000094')
end

.sequence_variant_causing_conservative_missense_codon_change_in_transcript ⇒ Object

The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position. (http://purl.obolibrary.org/obo/SO_1000060)

# File 'lib/biointerchange/so.rb', line 12773

def self.sequence_variant_causing_conservative_missense_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000060')
end

.sequence_variant_causing_cryptic_splice_acceptor_activation ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1001186)

# File 'lib/biointerchange/so.rb', line 13379

def self.sequence_variant_causing_cryptic_splice_acceptor_activation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001186')
end

.sequence_variant_causing_cryptic_splice_activation ⇒ Object

A sequence variant causing a new (functional) splice site. (http://purl.obolibrary.org/obo/SO_1000074)

# File 'lib/biointerchange/so.rb', line 12857

def self.sequence_variant_causing_cryptic_splice_activation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000074')
end

.sequence_variant_causing_cryptic_splice_donor_activation ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000186)

# File 'lib/biointerchange/so.rb', line 13373

def self.sequence_variant_causing_cryptic_splice_donor_activation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000186')
end

.sequence_variant_causing_gain_of_function_of_polypeptide ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000125)

# File 'lib/biointerchange/so.rb', line 13133

def self.sequence_variant_causing_gain_of_function_of_polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000125')
end

.sequence_variant_causing_gene_fusion ⇒ Object

A sequence_variant_effect that changes the gene structure by causing a fusion to another gene. (http://purl.obolibrary.org/obo/SO_1000181)

# File 'lib/biointerchange/so.rb', line 13343

def self.sequence_variant_causing_gene_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000181')
end

.sequence_variant_causing_inactive_catalytic_site ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000120)

# File 'lib/biointerchange/so.rb', line 13103

def self.sequence_variant_causing_inactive_catalytic_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000120')
end

.sequence_variant_causing_inactive_ligand_binding_site ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000119)

# File 'lib/biointerchange/so.rb', line 13097

def self.sequence_variant_causing_inactive_ligand_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000119')
end

.sequence_variant_causing_initiator_codon_change_in_transcript ⇒ Object

The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used. (http://purl.obolibrary.org/obo/SO_1000055)

# File 'lib/biointerchange/so.rb', line 12743

def self.sequence_variant_causing_initiator_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000055')
end

.sequence_variant_causing_loss_of_function_of_polypeptide ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000118)

# File 'lib/biointerchange/so.rb', line 13091

def self.sequence_variant_causing_loss_of_function_of_polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000118')
end

.sequence_variant_causing_minus_1_frameshift ⇒ Object

A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide. (http://purl.obolibrary.org/obo/SO_1000067)

# File 'lib/biointerchange/so.rb', line 12815

def self.sequence_variant_causing_minus_1_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000067')
end

.sequence_variant_causing_minus_2_frameshift ⇒ Object

A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides. (http://purl.obolibrary.org/obo/SO_1000069)

# File 'lib/biointerchange/so.rb', line 12827

def self.sequence_variant_causing_minus_2_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000069')
end

.sequence_variant_causing_missense_codon_change_in_transcript ⇒ Object

The nucleotide change in the codon leads to a new codon coding for a new amino acid. (http://purl.obolibrary.org/obo/SO_1000059)

# File 'lib/biointerchange/so.rb', line 12767

def self.sequence_variant_causing_missense_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000059')
end

.sequence_variant_causing_no_3D_structural_change ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is no effect, it is not a good term. (http://purl.obolibrary.org/obo/SO_1000112)

# File 'lib/biointerchange/so.rb', line 13067

def self.sequence_variant_causing_no_3D_structural_change
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000112')
end

.sequence_variant_causing_no_change_in_transcript ⇒ Object

No effect on the state of the RNA. (http://purl.obolibrary.org/obo/SO_1000050)

# File 'lib/biointerchange/so.rb', line 12731

def self.sequence_variant_causing_no_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000050')
end

.sequence_variant_causing_no_change_of_translational_product ⇒ Object

The sequence variant at RNA level does not lead to any change in polypeptide. (http://purl.obolibrary.org/obo/SO_1000089)

# File 'lib/biointerchange/so.rb', line 12941

def self.sequence_variant_causing_no_change_of_translational_product
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000089')
end

.sequence_variant_causing_non_synonymous_codon_change_in_transcript ⇒ Object

A DNA point mutation that causes a substitution of an amino acid by an other. (http://purl.obolibrary.org/obo/SO_1000058)

# File 'lib/biointerchange/so.rb', line 12761

def self.sequence_variant_causing_non_synonymous_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000058')
end

.sequence_variant_causing_nonconservative_amino_acid_substitution ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000095)

# File 'lib/biointerchange/so.rb', line 12965

def self.sequence_variant_causing_nonconservative_amino_acid_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000095')
end

.sequence_variant_causing_nonconservative_missense_codon_change_in_transcript ⇒ Object

The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position. (http://purl.obolibrary.org/obo/SO_1000061)

# File 'lib/biointerchange/so.rb', line 12779

def self.sequence_variant_causing_nonconservative_missense_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000061')
end

.sequence_variant_causing_nonsense_codon_change_in_transcript ⇒ Object

The nucleotide change in the codon triplet creates a terminator codon. (http://purl.obolibrary.org/obo/SO_1000062)

# File 'lib/biointerchange/so.rb', line 12785

def self.sequence_variant_causing_nonsense_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000062')
end

.sequence_variant_causing_partial_loss_of_function_of_polypeptide ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000124)

# File 'lib/biointerchange/so.rb', line 13127

def self.sequence_variant_causing_partial_loss_of_function_of_polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000124')
end

.sequence_variant_causing_plus_1_frameshift_mutation ⇒ Object

A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide. (http://purl.obolibrary.org/obo/SO_1000066)

# File 'lib/biointerchange/so.rb', line 12809

def self.sequence_variant_causing_plus_1_frameshift_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000066')
end

.sequence_variant_causing_plus_2_frameshift ⇒ Object

A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides. (http://purl.obolibrary.org/obo/SO_1000068)

# File 'lib/biointerchange/so.rb', line 12821

def self.sequence_variant_causing_plus_2_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000068')
end

.sequence_variant_causing_polypeptide_elongation ⇒ Object

The extension of the translational product at either (or both) the N-terminus and/or the C-terminus. (http://purl.obolibrary.org/obo/SO_1000099)

# File 'lib/biointerchange/so.rb', line 12989

def self.sequence_variant_causing_polypeptide_elongation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000099')
end

.sequence_variant_causing_polypeptide_fusion ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000134)

# File 'lib/biointerchange/so.rb', line 13157

def self.sequence_variant_causing_polypeptide_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000134')
end

.sequence_variant_causing_polypeptide_localization_change ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000121)

# File 'lib/biointerchange/so.rb', line 13109

def self.sequence_variant_causing_polypeptide_localization_change
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000121')
end

.sequence_variant_causing_polypeptide_post_translational_processing_change ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000122)

# File 'lib/biointerchange/so.rb', line 13115

def self.sequence_variant_causing_polypeptide_post_translational_processing_change
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000122')
end

.sequence_variant_causing_polypeptide_truncation ⇒ Object

The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062). (http://purl.obolibrary.org/obo/SO_1000098)

# File 'lib/biointerchange/so.rb', line 12983

def self.sequence_variant_causing_polypeptide_truncation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000098')
end

.sequence_variant_causing_synonymous_codon_change_in_transcript ⇒ Object

The changed codon has the same translation product as the original codon. (http://purl.obolibrary.org/obo/SO_1000057)

# File 'lib/biointerchange/so.rb', line 12755

def self.sequence_variant_causing_synonymous_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000057')
end

.sequence_variant_causing_terminator_codon_change_in_transcript ⇒ Object

The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence. (http://purl.obolibrary.org/obo/SO_1000063)

# File 'lib/biointerchange/so.rb', line 12791

def self.sequence_variant_causing_terminator_codon_change_in_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000063')
end

.sequence_variant_decreasing_level_of_translation_product ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000103)

# File 'lib/biointerchange/so.rb', line 13013

def self.sequence_variant_decreasing_level_of_translation_product
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000103')
end

.sequence_variant_decreasing_rate_of_transcription ⇒ Object

A sequence variation that decreases the rate a which transcription of the sequence occurs. (http://purl.obolibrary.org/obo/SO_1000078)

# File 'lib/biointerchange/so.rb', line 12875

def self.sequence_variant_decreasing_rate_of_transcription
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000078')
end

.sequence_variant_decreasing_transcript_stability ⇒ Object

Sequence variant decreases the stability (half-life) of the transcript. (http://purl.obolibrary.org/obo/SO_1000084)

# File 'lib/biointerchange/so.rb', line 12911

def self.sequence_variant_decreasing_transcript_stability
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000084')
end

.sequence_variant_effect ⇒ Object

The effect of a change in nucleotide sequence. (http://purl.obolibrary.org/obo/SO_1000132)

# File 'lib/biointerchange/so.rb', line 13151

def self.sequence_variant_effect
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000132')
end

.sequence_variant_increasing_level_of_translation_product ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000104)

# File 'lib/biointerchange/so.rb', line 13019

def self.sequence_variant_increasing_level_of_translation_product
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000104')
end

.sequence_variant_increasing_rate_of_transcription ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000080)

# File 'lib/biointerchange/so.rb', line 12887

def self.sequence_variant_increasing_rate_of_transcription
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000080')
end

.sequence_variant_increasing_transcript_stability ⇒ Object

Sequence variant increases the stability (half-life) of the transcript. (http://purl.obolibrary.org/obo/SO_1000083)

# File 'lib/biointerchange/so.rb', line 12905

def self.sequence_variant_increasing_transcript_stability
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000083')
end

.sequence_variant_obs ⇒ Object

A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. (http://purl.obolibrary.org/obo/SO_0000109)

# File 'lib/biointerchange/so.rb', line 971

def self.sequence_variant_obs
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000109')
end

.sequence_variation_affecting_coding_sequence ⇒ Object

Any of the amino acid coding triplets of a gene are affected by the DNA mutation. (http://purl.obolibrary.org/obo/SO_1000054)

# File 'lib/biointerchange/so.rb', line 12737

def self.sequence_variation_affecting_coding_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000054')
end

.sequence_variation_affecting_level_of_transcript ⇒ Object

A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. (http://purl.obolibrary.org/obo/SO_1000085)

# File 'lib/biointerchange/so.rb', line 12917

def self.sequence_variation_affecting_level_of_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000085')
end

.sequence_variation_affecting_reading_frame ⇒ Object

An umbrella term for terms describing an effect of a sequence variation on the frame of translation. (http://purl.obolibrary.org/obo/SO_1000064)

# File 'lib/biointerchange/so.rb', line 12797

def self.sequence_variation_affecting_reading_frame
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000064')
end

.sequence_variation_affecting_transcript ⇒ Object

Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. (http://purl.obolibrary.org/obo/SO_1000049)

# File 'lib/biointerchange/so.rb', line 12725

def self.sequence_variation_affecting_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000049')
end

.sequence_variation_affecting_transcript_sequence ⇒ Object

OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. (http://purl.obolibrary.org/obo/SO_1000079)

# File 'lib/biointerchange/so.rb', line 12881

def self.sequence_variation_affecting_transcript_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000079')
end

.sequence_variation_decreasing_level_of_transcript ⇒ Object

A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. (http://purl.obolibrary.org/obo/SO_1000086)

# File 'lib/biointerchange/so.rb', line 12923

def self.sequence_variation_decreasing_level_of_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000086')
end

.sequence_variation_increasing_level_of_transcript ⇒ Object

A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. (http://purl.obolibrary.org/obo/SO_1000087)

# File 'lib/biointerchange/so.rb', line 12929

def self.sequence_variation_increasing_level_of_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000087')
end

.sequencing_primer ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000107)

# File 'lib/biointerchange/so.rb', line 959

def self.sequencing_primer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000107')
end

.serine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001444)

# File 'lib/biointerchange/so.rb', line 8923

def self.serine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001444')
end

.serine_threonine_motif ⇒ Object

A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4). (http://purl.obolibrary.org/obo/SO_0001126)

# File 'lib/biointerchange/so.rb', line 7027

def self.serine_threonine_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001126')
end

.serine_threonine_staple_motif ⇒ Object

A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative. (http://purl.obolibrary.org/obo/SO_0001127)

# File 'lib/biointerchange/so.rb', line 7033

def self.serine_threonine_staple_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001127')
end

.serine_threonine_turn ⇒ Object

A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2). (http://purl.obolibrary.org/obo/SO_0001141)

# File 'lib/biointerchange/so.rb', line 7117

def self.serine_threonine_turn
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001141')
end

.serine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding seryl tRNA (SO:000269). (http://purl.obolibrary.org/obo/SO_0000226)

# File 'lib/biointerchange/so.rb', line 1677

def self.serine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000226')
end

.seryl_tRNA ⇒ Object

A tRNA sequence that has a serine anticodon, and a 3' serine binding region. (http://purl.obolibrary.org/obo/SO_0000269)

# File 'lib/biointerchange/so.rb', line 1935

def self.seryl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000269')
end

.seven_aminomethyl_seven_deazaguanosine ⇒ Object

7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine. (http://purl.obolibrary.org/obo/SO_0001322)

# File 'lib/biointerchange/so.rb', line 8197

def self.seven_aminomethyl_seven_deazaguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001322')
end

.seven_cyano_seven_deazaguanosine ⇒ Object

7_cyano_7_deazaguanosine is a modified 7-deazoguanosine. (http://purl.obolibrary.org/obo/SO_0001321)

# File 'lib/biointerchange/so.rb', line 8191

def self.seven_cyano_seven_deazaguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001321')
end

.seven_deazaguanosine ⇒ Object

7-deazaguanosine is a moddified guanosine. (http://purl.obolibrary.org/obo/SO_0001316)

# File 'lib/biointerchange/so.rb', line 8161

def self.seven_deazaguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001316')
end

.seven_methylguanine ⇒ Object

A modified RNA base in which guanine is methylated at the 7- position. (http://purl.obolibrary.org/obo/SO_0001231)

# File 'lib/biointerchange/so.rb', line 7657

def self.seven_methylguanine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001231')
end

.seven_methylguanosine ⇒ Object

7_methylguanosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001326)

# File 'lib/biointerchange/so.rb', line 8221

def self.seven_methylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001326')
end

.sgRNA ⇒ Object

A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method. (http://purl.obolibrary.org/obo/SO_0001998)

# File 'lib/biointerchange/so.rb', line 12191

def self.sgRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001998')
end

.shadow_enhancer ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001482)

# File 'lib/biointerchange/so.rb', line 9151

def self.shadow_enhancer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001482')
end

.Shine_Dalgarno_sequence ⇒ Object

A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex. (http://purl.obolibrary.org/obo/SO_0000552)

# File 'lib/biointerchange/so.rb', line 3631

def self.Shine_Dalgarno_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000552')
end

.signal_anchor ⇒ Object

A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane. (http://purl.obolibrary.org/obo/SO_0001809)

# File 'lib/biointerchange/so.rb', line 11059

def self.signal_anchor
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001809')
end

.signal_peptide ⇒ Object

The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components. (http://purl.obolibrary.org/obo/SO_0000418)

# File 'lib/biointerchange/so.rb', line 2823

def self.signal_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000418')
end

.signature ⇒ Object

A region of sequence where developer information is encoded. (http://purl.obolibrary.org/obo/SO_0001978)

# File 'lib/biointerchange/so.rb', line 12077

def self.signature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001978')
end

.silenced ⇒ Object

An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level. (http://purl.obolibrary.org/obo/SO_0000893)

# File 'lib/biointerchange/so.rb', line 5639

def self.silenced
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000893')
end

.silenced_by_DNA_methylation ⇒ Object

An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription. (http://purl.obolibrary.org/obo/SO_0000895)

# File 'lib/biointerchange/so.rb', line 5651

def self.silenced_by_DNA_methylation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000895')
end

.silenced_by_DNA_modification ⇒ Object

An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription. (http://purl.obolibrary.org/obo/SO_0000894)

# File 'lib/biointerchange/so.rb', line 5645

def self.silenced_by_DNA_modification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000894')
end

.silenced_by_histone_deacetylation ⇒ Object

An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation. (http://purl.obolibrary.org/obo/SO_0001223)

# File 'lib/biointerchange/so.rb', line 7609

def self.silenced_by_histone_deacetylation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001223')
end

.silenced_by_histone_methylation ⇒ Object

An attribute describing an epigenetic process where a gene is inactivated by histone methylation. (http://purl.obolibrary.org/obo/SO_0001222)

# File 'lib/biointerchange/so.rb', line 7603

def self.silenced_by_histone_methylation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001222')
end

.silenced_by_histone_modification ⇒ Object

An attribute describing an epigenetic process where a gene is inactivated by histone modification. (http://purl.obolibrary.org/obo/SO_0001221)

# File 'lib/biointerchange/so.rb', line 7597

def self.silenced_by_histone_modification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001221')
end

.silenced_by_RNA_interference ⇒ Object

An attribute describing an epigenetic process where a gene is inactivated by RNA interference. (http://purl.obolibrary.org/obo/SO_0001220)

# File 'lib/biointerchange/so.rb', line 7591

def self.silenced_by_RNA_interference
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001220')
end

.silenced_gene ⇒ Object

A gene that is silenced. (http://purl.obolibrary.org/obo/SO_0000127)

# File 'lib/biointerchange/so.rb', line 1079

def self.silenced_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000127')
end

.silencer ⇒ Object

A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control. (http://purl.obolibrary.org/obo/SO_0000625)

# File 'lib/biointerchange/so.rb', line 4073

def self.silencer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000625')
end

.silent_mating_type_cassette_array ⇒ Object

A gene cassette array that corresponds to a silenced version of a mating type region. (http://purl.obolibrary.org/obo/SO_0001984)

# File 'lib/biointerchange/so.rb', line 12107

def self.silent_mating_type_cassette_array
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001984')
end

.silent_mutation ⇒ Object

A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation. (http://purl.obolibrary.org/obo/SO_0001017)

# File 'lib/biointerchange/so.rb', line 6377

def self.silent_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001017')
end

.similar_to ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#similar_to)

# File 'lib/biointerchange/so.rb', line 251

def self.similar_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#similar_to')
end

.simple_sequence_length_variation ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000207)

# File 'lib/biointerchange/so.rb', line 1563

def self.simple_sequence_length_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000207')
end

.SINE_element ⇒ Object

A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element. (http://purl.obolibrary.org/obo/SO_0000206)

# File 'lib/biointerchange/so.rb', line 1557

def self.SINE_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000206')
end

.single ⇒ Object

Attributes added to describe the different kinds of replicon. SO workshop, September 2006. (http://purl.obolibrary.org/obo/SO_0000984)

# File 'lib/biointerchange/so.rb', line 6179

def self.single
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000984')
end

.single_strand_restriction_enzyme_cleavage_site ⇒ Object

A restriction enzyme cleavage site whereby only one strand is cut. (http://purl.obolibrary.org/obo/SO_0001694)

# File 'lib/biointerchange/so.rb', line 10375

def self.single_strand_restriction_enzyme_cleavage_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001694')
end

.single_stranded_cDNA ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000757)

# File 'lib/biointerchange/so.rb', line 4865

def self.single_stranded_cDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000757')
end

.single_stranded_DNA_chromosome ⇒ Object

Structural unit composed of a self-replicating, single-stranded DNA molecule. (http://purl.obolibrary.org/obo/SO_0000956)

# File 'lib/biointerchange/so.rb', line 6017

def self.single_stranded_DNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000956')
end

.single_stranded_RNA_chromosome ⇒ Object

Structural unit composed of a self-replicating, single-stranded RNA molecule. (http://purl.obolibrary.org/obo/SO_0000962)

# File 'lib/biointerchange/so.rb', line 6053

def self.single_stranded_RNA_chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000962')
end

.siRNA ⇒ Object

A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules. (http://purl.obolibrary.org/obo/SO_0000646)

# File 'lib/biointerchange/so.rb', line 4199

def self.siRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000646')
end

.site ⇒ Object

The interbase position where something (eg an aberration) occurred. (http://purl.obolibrary.org/obo/SO_0000408)

# File 'lib/biointerchange/so.rb', line 2763

def self.site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000408')
end

.site_specific_recombination_target_region ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000342)

# File 'lib/biointerchange/so.rb', line 2373

def self.site_specific_recombination_target_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000342')
end

.six_cutter_restriction_site ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000249)

# File 'lib/biointerchange/so.rb', line 1815

def self.six_cutter_restriction_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000249')
end

.SL10_acceptor_site ⇒ Object

A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts. (http://purl.obolibrary.org/obo/SO_0001755)

# File 'lib/biointerchange/so.rb', line 10741

def self.SL10_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001755')
end

.SL11_acceptor_site ⇒ Object

A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts. (http://purl.obolibrary.org/obo/SO_0001756)

# File 'lib/biointerchange/so.rb', line 10747

def self.SL11_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001756')
end

.SL12_acceptor_site ⇒ Object

A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts. (http://purl.obolibrary.org/obo/SO_0001757)

# File 'lib/biointerchange/so.rb', line 10753

def self.SL12_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001757')
end

.SL1_acceptor_site ⇒ Object

A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs. (http://purl.obolibrary.org/obo/SO_0000708)

# File 'lib/biointerchange/so.rb', line 4571

def self.SL1_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000708')
end

.SL2_acceptor_site ⇒ Object

A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts. (http://purl.obolibrary.org/obo/SO_0000709)

# File 'lib/biointerchange/so.rb', line 4577

def self.SL2_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000709')
end

.SL3_acceptor_site ⇒ Object

A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts. (http://purl.obolibrary.org/obo/SO_0001748)

# File 'lib/biointerchange/so.rb', line 10699

def self.SL3_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001748')
end

.SL4_acceptor_site ⇒ Object

A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts. (http://purl.obolibrary.org/obo/SO_0001749)

# File 'lib/biointerchange/so.rb', line 10705

def self.SL4_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001749')
end

.SL5_acceptor_site ⇒ Object

A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts. (http://purl.obolibrary.org/obo/SO_0001750)

# File 'lib/biointerchange/so.rb', line 10711

def self.SL5_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001750')
end

.SL6_acceptor_site ⇒ Object

A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts. (http://purl.obolibrary.org/obo/SO_0001751)

# File 'lib/biointerchange/so.rb', line 10717

def self.SL6_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001751')
end

.SL7_acceptor_site ⇒ Object

A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts. (http://purl.obolibrary.org/obo/SO_0001752)

# File 'lib/biointerchange/so.rb', line 10723

def self.SL7_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001752')
end

.SL8_acceptor_site ⇒ Object

A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts. (http://purl.obolibrary.org/obo/SO_0001753)

# File 'lib/biointerchange/so.rb', line 10729

def self.SL8_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001753')
end

.SL9_acceptor_site ⇒ Object

A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts. (http://purl.obolibrary.org/obo/SO_0001754)

# File 'lib/biointerchange/so.rb', line 10735

def self.SL9_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001754')
end

.small_regulatory_ncRNA ⇒ Object

A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression. (http://purl.obolibrary.org/obo/SO_0000370)

# File 'lib/biointerchange/so.rb', line 2535

def self.small_regulatory_ncRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000370')
end

.small_subunit_rRNA ⇒ Object

Ribosomal RNA transcript that structures the small subunit of the ribosome. (http://purl.obolibrary.org/obo/SO_0000650)

# File 'lib/biointerchange/so.rb', line 4223

def self.small_subunit_rRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000650')
end

.smFISH_probe ⇒ Object

A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment. (http://purl.obolibrary.org/obo/SO_0001854)

# File 'lib/biointerchange/so.rb', line 11329

def self.smFISH_probe
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001854')
end

.snoRNA ⇒ Object

A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA. (http://purl.obolibrary.org/obo/SO_0000275)

# File 'lib/biointerchange/so.rb', line 1971

def self.snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000275')
end

.snoRNA_encoding ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000578)

# File 'lib/biointerchange/so.rb', line 3791

def self.snoRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000578')
end

.snoRNA_gene ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001267)

# File 'lib/biointerchange/so.rb', line 7867

def self.snoRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001267')
end

.snoRNA_primary_transcript ⇒ Object

A primary transcript encoding a small nucleolar mRNA (SO:0000275). (http://purl.obolibrary.org/obo/SO_0000232)

# File 'lib/biointerchange/so.rb', line 1713

def self.snoRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000232')
end

.SNP ⇒ Object

SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater. (http://purl.obolibrary.org/obo/SO_0000694)

# File 'lib/biointerchange/so.rb', line 4487

def self.SNP
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000694')
end

.snRNA ⇒ Object

A small nuclear RNA molecule involved in pre-mRNA splicing and processing. (http://purl.obolibrary.org/obo/SO_0000274)

# File 'lib/biointerchange/so.rb', line 1965

def self.snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000274')
end

.snRNA_encoding ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000623)

# File 'lib/biointerchange/so.rb', line 4061

def self.snRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000623')
end

.snRNA_gene ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001268)

# File 'lib/biointerchange/so.rb', line 7873

def self.snRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001268')
end

.snRNA_primary_transcript ⇒ Object

A primary transcript encoding a small nuclear RNA (SO:0000274). (http://purl.obolibrary.org/obo/SO_0000231)

# File 'lib/biointerchange/so.rb', line 1707

def self.snRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000231')
end

.SNV ⇒ Object

SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist. (http://purl.obolibrary.org/obo/SO_0001483)

# File 'lib/biointerchange/so.rb', line 9157

def self.SNV
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001483')
end

.solo_LTR ⇒ Object

A recombination product between the 2 LTR of the same element. (http://purl.obolibrary.org/obo/SO_0001003)

# File 'lib/biointerchange/so.rb', line 6293

def self.solo_LTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001003')
end

.somatic_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001777)

# File 'lib/biointerchange/so.rb', line 10873

def self.somatic_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001777')
end

.sonicate_fragment ⇒ Object

A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments. (http://purl.obolibrary.org/obo/SO_0001253)

# File 'lib/biointerchange/so.rb', line 7783

def self.sonicate_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001253')
end

.SP6_RNA_Polymerase_Promoter ⇒ Object

A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription. (http://purl.obolibrary.org/obo/SO_0001205)

# File 'lib/biointerchange/so.rb', line 7501

def self.SP6_RNA_Polymerase_Promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001205')
end

.specific_recombination_site ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000299)

# File 'lib/biointerchange/so.rb', line 2115

def self.specific_recombination_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000299')
end

.splice_acceptor_variant ⇒ Object

A splice variant that changes the 2 base region at the 3' end of an intron. (http://purl.obolibrary.org/obo/SO_0001574)

# File 'lib/biointerchange/so.rb', line 9703

def self.splice_acceptor_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001574')
end

.splice_donor_5th_base_variant ⇒ Object

A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript. (http://purl.obolibrary.org/obo/SO_0001787)

# File 'lib/biointerchange/so.rb', line 10927

def self.splice_donor_5th_base_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001787')
end

.splice_donor_variant ⇒ Object

A splice variant that changes the 2 base pair region at the 5' end of an intron. (http://purl.obolibrary.org/obo/SO_0001575)

# File 'lib/biointerchange/so.rb', line 9709

def self.splice_donor_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001575')
end

.splice_enhancer ⇒ Object

Region of a transcript that regulates splicing. (http://purl.obolibrary.org/obo/SO_0000344)

# File 'lib/biointerchange/so.rb', line 2385

def self.splice_enhancer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000344')
end

.splice_junction ⇒ Object

The boundary between an intron and an exon. (http://purl.obolibrary.org/obo/SO_0001421)

# File 'lib/biointerchange/so.rb', line 8791

def self.splice_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001421')
end

.splice_region ⇒ Object

A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. (http://purl.obolibrary.org/obo/SO_0001902)

# File 'lib/biointerchange/so.rb', line 11617

def self.splice_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001902')
end

.splice_region_variant ⇒ Object

A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. (http://purl.obolibrary.org/obo/SO_0001630)

# File 'lib/biointerchange/so.rb', line 10015

def self.splice_region_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001630')
end

.splice_site ⇒ Object

Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction. (http://purl.obolibrary.org/obo/SO_0000162)

# File 'lib/biointerchange/so.rb', line 1289

def self.splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000162')
end

.splice_site_variant ⇒ Object

A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript. (http://purl.obolibrary.org/obo/SO_0001629)

# File 'lib/biointerchange/so.rb', line 10009

def self.splice_site_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001629')
end

.spliced_leader_RNA ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000636)

# File 'lib/biointerchange/so.rb', line 4139

def self.spliced_leader_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000636')
end

.spliceosomal_intron ⇒ Object

An intron which is spliced by the spliceosome. (http://purl.obolibrary.org/obo/SO_0000662)

# File 'lib/biointerchange/so.rb', line 4295

def self.spliceosomal_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000662')
end

.spliceosomal_intron_region ⇒ Object

A region within an intron. (http://purl.obolibrary.org/obo/SO_0000841)

# File 'lib/biointerchange/so.rb', line 5327

def self.spliceosomal_intron_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000841')
end

.splicing_feature ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000682)

# File 'lib/biointerchange/so.rb', line 4415

def self.splicing_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000682')
end

.splicing_regulatory_region ⇒ Object

A regulatory_region that modulates splicing. (http://purl.obolibrary.org/obo/SO_0001056)

# File 'lib/biointerchange/so.rb', line 6619

def self.splicing_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001056')
end

.splicing_variant ⇒ Object

A sequence variant that changes the process of splicing. (http://purl.obolibrary.org/obo/SO_0001568)

# File 'lib/biointerchange/so.rb', line 9667

def self.splicing_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001568')
end

.spot_42_RNA ⇒ Object

A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels. (http://purl.obolibrary.org/obo/SO_0000389)

# File 'lib/biointerchange/so.rb', line 2649

def self.spot_42_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000389')
end

.SRP_RNA ⇒ Object

The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding. (http://purl.obolibrary.org/obo/SO_0000590)

# File 'lib/biointerchange/so.rb', line 3863

def self.SRP_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000590')
end

.SRP_RNA_encoding ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000642)

# File 'lib/biointerchange/so.rb', line 4175

def self.SRP_RNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000642')
end

.SRP_RNA_gene ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001269)

# File 'lib/biointerchange/so.rb', line 7879

def self.SRP_RNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001269')
end

.SRP_RNA_primary_transcript ⇒ Object

A primary transcript encoding a signal recognition particle RNA. (http://purl.obolibrary.org/obo/SO_0000589)

# File 'lib/biointerchange/so.rb', line 3857

def self.SRP_RNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000589')
end

.ss_oligo ⇒ Object

A single stranded oligonucleotide. (http://purl.obolibrary.org/obo/SO_0000441)

# File 'lib/biointerchange/so.rb', line 2965

def self.ss_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000441')
end

.ss_RNA_viral_sequence ⇒ Object

A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA. (http://purl.obolibrary.org/obo/SO_0001199)

# File 'lib/biointerchange/so.rb', line 7465

def self.ss_RNA_viral_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001199')
end

.st_turn_left_handed_type_one ⇒ Object

The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees. (http://purl.obolibrary.org/obo/SO_0001142)

# File 'lib/biointerchange/so.rb', line 7123

def self.st_turn_left_handed_type_one
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001142')
end

.st_turn_left_handed_type_two ⇒ Object

The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees. (http://purl.obolibrary.org/obo/SO_0001143)

# File 'lib/biointerchange/so.rb', line 7129

def self.st_turn_left_handed_type_two
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001143')
end

.st_turn_right_handed_type_one ⇒ Object

The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees. (http://purl.obolibrary.org/obo/SO_0001144)

# File 'lib/biointerchange/so.rb', line 7135

def self.st_turn_right_handed_type_one
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001144')
end

.st_turn_right_handed_type_two ⇒ Object

The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees. (http://purl.obolibrary.org/obo/SO_0001145)

# File 'lib/biointerchange/so.rb', line 7141

def self.st_turn_right_handed_type_two
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001145')
end

.standard_draft ⇒ Object

The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete. (http://purl.obolibrary.org/obo/SO_0001486)

# File 'lib/biointerchange/so.rb', line 9175

def self.standard_draft
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001486')
end

.start_codon ⇒ Object

First codon to be translated by a ribosome. (http://purl.obolibrary.org/obo/SO_0000318)

# File 'lib/biointerchange/so.rb', line 2229

def self.start_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000318')
end

.started_by ⇒ Object

X is strted_by Y if Y is part_of X and X and Y share a 5' boundary. (http://purl.obolibrary.org/obo/so_2_5_2.obo#started_by)

# File 'lib/biointerchange/so.rb', line 257

def self.started_by
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#started_by')
end

.starts ⇒ Object

X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary. (http://purl.obolibrary.org/obo/so_2_5_2.obo#starts)

# File 'lib/biointerchange/so.rb', line 263

def self.starts
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#starts')
end

.status ⇒ Object

An attribute describing the status of a feature, based on the available evidence. (http://purl.obolibrary.org/obo/SO_0000905)

# File 'lib/biointerchange/so.rb', line 5711

def self.status
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000905')
end

.status_of_coding_sequence ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_1001255)

# File 'lib/biointerchange/so.rb', line 13493

def self.status_of_coding_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001255')
end

.stem_loop ⇒ Object

A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences. (http://purl.obolibrary.org/obo/SO_0000313)

# File 'lib/biointerchange/so.rb', line 2199

def self.stem_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000313')
end

.sterol_regulatory_element ⇒ Object

A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs. (http://purl.obolibrary.org/obo/SO_0001861)

# File 'lib/biointerchange/so.rb', line 11371

def self.sterol_regulatory_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001861')
end

.sticky_end_restriction_enzyme_cleavage_site ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001692)

# File 'lib/biointerchange/so.rb', line 10363

def self.sticky_end_restriction_enzyme_cleavage_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001692')
end

.stop_codon ⇒ Object

In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis. (http://purl.obolibrary.org/obo/SO_0000319)

# File 'lib/biointerchange/so.rb', line 2235

def self.stop_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000319')
end

.stop_codon_read_through ⇒ Object

A stop codon redefined to be a new amino acid. (http://purl.obolibrary.org/obo/SO_0000883)

# File 'lib/biointerchange/so.rb', line 5579

def self.stop_codon_read_through
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000883')
end

.stop_codon_readthrough ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_1001267)

# File 'lib/biointerchange/so.rb', line 13547

def self.stop_codon_readthrough
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001267')
end

.stop_codon_redefined_as_pyrrolysine ⇒ Object

A stop codon redefined to be the new amino acid, pyrrolysine. (http://purl.obolibrary.org/obo/SO_0000884)

# File 'lib/biointerchange/so.rb', line 5585

def self.stop_codon_redefined_as_pyrrolysine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000884')
end

.stop_codon_redefined_as_selenocysteine ⇒ Object

A stop codon redefined to be the new amino acid, selenocysteine. (http://purl.obolibrary.org/obo/SO_0000885)

# File 'lib/biointerchange/so.rb', line 5591

def self.stop_codon_redefined_as_selenocysteine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000885')
end

.stop_codon_redefinition_as_pyrrolysine ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_1001270)

# File 'lib/biointerchange/so.rb', line 13565

def self.stop_codon_redefinition_as_pyrrolysine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001270')
end

.stop_codon_redefinition_as_selenocysteine ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_1001266)

# File 'lib/biointerchange/so.rb', line 13541

def self.stop_codon_redefinition_as_selenocysteine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001266')
end

.stop_codon_signal ⇒ Object

A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding. (http://purl.obolibrary.org/obo/SO_1001288)

# File 'lib/biointerchange/so.rb', line 13661

def self.stop_codon_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001288')
end

.stop_gained ⇒ Object

A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript. (http://purl.obolibrary.org/obo/SO_0001587)

# File 'lib/biointerchange/so.rb', line 9769

def self.stop_gained
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001587')
end

.stop_lost ⇒ Object

A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript. (http://purl.obolibrary.org/obo/SO_0001578)

# File 'lib/biointerchange/so.rb', line 9727

def self.stop_lost
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001578')
end

.stop_retained_variant ⇒ Object

A sequence variant where at least one base in the terminator codon is changed, but the terminator remains. (http://purl.obolibrary.org/obo/SO_0001567)

# File 'lib/biointerchange/so.rb', line 9661

def self.stop_retained_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001567')
end

.strand_attribute ⇒ Object

Attributes added to describe the different kinds of replicon. SO workshop, September 2006. (http://purl.obolibrary.org/obo/SO_0000983)

# File 'lib/biointerchange/so.rb', line 6173

def self.strand_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000983')
end

.STREP_motif ⇒ Object

A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2. (http://purl.obolibrary.org/obo/SO_0001859)

# File 'lib/biointerchange/so.rb', line 11359

def self.STREP_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001859')
end

.stRNA ⇒ Object

Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans. (http://purl.obolibrary.org/obo/SO_0000649)

# File 'lib/biointerchange/so.rb', line 4217

def self.stRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000649')
end

.stRNA_encoding ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000656)

# File 'lib/biointerchange/so.rb', line 4259

def self.stRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000656')
end

.stRNA_gene ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001270)

# File 'lib/biointerchange/so.rb', line 7885

def self.stRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001270')
end

.stRNA_primary_transcript ⇒ Object

A primary transcript encoding a small temporal mRNA (SO:0000649). (http://purl.obolibrary.org/obo/SO_0000648)

# File 'lib/biointerchange/so.rb', line 4211

def self.stRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000648')
end

.structural_alteration ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001785)

# File 'lib/biointerchange/so.rb', line 10915

def self.structural_alteration
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001785')
end

.structural_variant ⇒ Object

A sequence variant that changes one or more sequence features. (http://purl.obolibrary.org/obo/SO_0001537)

# File 'lib/biointerchange/so.rb', line 9481

def self.structural_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001537')
end

.STS ⇒ Object

Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known. (http://purl.obolibrary.org/obo/SO_0000331)

# File 'lib/biointerchange/so.rb', line 2307

def self.STS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000331')
end

.STS_map ⇒ Object

An STS map is a physical map organized by the unique STS landmarks. (http://purl.obolibrary.org/obo/SO_0001251)

# File 'lib/biointerchange/so.rb', line 7771

def self.STS_map
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001251')
end

.substitute ⇒ Object

To substitute a subsection of sequence for another. (http://purl.obolibrary.org/obo/SO_0000048)

# File 'lib/biointerchange/so.rb', line 597

def self.substitute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000048')
end

.substitute_A_to_I ⇒ Object

An edit to substitute an I for an A. (http://purl.obolibrary.org/obo/SO_0000919)

# File 'lib/biointerchange/so.rb', line 5795

def self.substitute_A_to_I
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000919')
end

.substitute_C_to_U ⇒ Object

An edit to substitute an U for a C. (http://purl.obolibrary.org/obo/SO_0000922)

# File 'lib/biointerchange/so.rb', line 5813

def self.substitute_C_to_U
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000922')
end

.substitution ⇒ Object

A sequence alteration where the length of the change in the variant is the same as that of the reference. (http://purl.obolibrary.org/obo/SO_1000002)

# File 'lib/biointerchange/so.rb', line 12479

def self.substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000002')
end

.subtelomere ⇒ Object

A heterochromatic region of the chromosome, adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed. (http://purl.obolibrary.org/obo/SO_0001997)

# File 'lib/biointerchange/so.rb', line 12185

def self.subtelomere
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001997')
end

.sugar_edge_base_pair ⇒ Object

A type of non-canonical base-pairing. (http://purl.obolibrary.org/obo/SO_0000030)

# File 'lib/biointerchange/so.rb', line 489

def self.sugar_edge_base_pair
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000030')
end

.supercontig ⇒ Object

One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. (http://purl.obolibrary.org/obo/SO_0000148)

# File 'lib/biointerchange/so.rb', line 1205

def self.supercontig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000148')
end

.supported_by_domain_match ⇒ Object

An attribute to describe a feature that has been predicted using sequence similarity of a known domain. (http://purl.obolibrary.org/obo/SO_0000908)

# File 'lib/biointerchange/so.rb', line 5729

def self.supported_by_domain_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000908')
end

.supported_by_EST_or_cDNA ⇒ Object

An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data. (http://purl.obolibrary.org/obo/SO_0000909)

# File 'lib/biointerchange/so.rb', line 5735

def self.supported_by_EST_or_cDNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000909')
end

.supported_by_sequence_similarity ⇒ Object

An attribute to describe a feature that has been predicted using sequence similarity techniques. (http://purl.obolibrary.org/obo/SO_0000907)

# File 'lib/biointerchange/so.rb', line 5723

def self.supported_by_sequence_similarity
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000907')
end

.symbiosis_island ⇒ Object

A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria. (http://purl.obolibrary.org/obo/SO_0000776)

# File 'lib/biointerchange/so.rb', line 4973

def self.symbiosis_island
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000776')
end

.symmetric_RNA_internal_loop ⇒ Object

An internal RNA loop where the extent of the loop on both stands is the same size. (http://purl.obolibrary.org/obo/SO_0000025)

# File 'lib/biointerchange/so.rb', line 459

def self.symmetric_RNA_internal_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000025')
end

.synonymous ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001815)

# File 'lib/biointerchange/so.rb', line 11095

def self.synonymous
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001815')
end

.synonymous_variant ⇒ Object

A sequence variant where there is no resulting change to the encoded amino acid. (http://purl.obolibrary.org/obo/SO_0001819)

# File 'lib/biointerchange/so.rb', line 11119

def self.synonymous_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001819')
end

.syntenic ⇒ Object

Attribute describing sequence regions occurring in same order on chromosome of different species. (http://purl.obolibrary.org/obo/SO_0000860)

# File 'lib/biointerchange/so.rb', line 5441

def self.syntenic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000860')
end

.syntenic_region ⇒ Object

A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species. (http://purl.obolibrary.org/obo/SO_0005858)

# File 'lib/biointerchange/so.rb', line 12347

def self.syntenic_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005858')
end

.synthetic_oligo ⇒ Object

An oligo composed of synthetic nucleotides. (http://purl.obolibrary.org/obo/SO_0001247)

# File 'lib/biointerchange/so.rb', line 7747

def self.synthetic_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001247')
end

.synthetic_sequence ⇒ Object

An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence. (http://purl.obolibrary.org/obo/SO_0000351)

# File 'lib/biointerchange/so.rb', line 2427

def self.synthetic_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000351')
end

.T3_RNA_Polymerase_Promoter ⇒ Object

A DNA sequence to which the T3 RNA polymerase binds, to begin transcription. (http://purl.obolibrary.org/obo/SO_0001206)

# File 'lib/biointerchange/so.rb', line 7507

def self.T3_RNA_Polymerase_Promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001206')
end

.T7_RNA_Polymerase_Promoter ⇒ Object

A region (DNA) to which the T7 RNA polymerase binds, to begin transcription. (http://purl.obolibrary.org/obo/SO_0001207)

# File 'lib/biointerchange/so.rb', line 7513

def self.T7_RNA_Polymerase_Promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001207')
end

.T_loop ⇒ Object

Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C. (http://purl.obolibrary.org/obo/SO_0001177)

# File 'lib/biointerchange/so.rb', line 7333

def self.T_loop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001177')
end

.T_to_A_transversion ⇒ Object

A transversion from T to A. (http://purl.obolibrary.org/obo/SO_1000021)

# File 'lib/biointerchange/so.rb', line 12569

def self.T_to_A_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000021')
end

.T_to_C_transition ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_1000013)

# File 'lib/biointerchange/so.rb', line 12521

def self.T_to_C_transition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000013')
end

.T_to_G_transversion ⇒ Object

A transversion from T to G. (http://purl.obolibrary.org/obo/SO_1000022)

# File 'lib/biointerchange/so.rb', line 12575

def self.T_to_G_transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000022')
end

.tag ⇒ Object

A nucleotide sequence that may be used to identify a larger sequence. (http://purl.obolibrary.org/obo/SO_0000324)

# File 'lib/biointerchange/so.rb', line 2265

def self.tag
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000324')
end

.tandem ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001513)

# File 'lib/biointerchange/so.rb', line 9337

def self.tandem
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001513')
end

.tandem_duplication ⇒ Object

A duplication consisting of 2 identical adjacent regions. (http://purl.obolibrary.org/obo/SO_1000173)

# File 'lib/biointerchange/so.rb', line 13325

def self.tandem_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000173')
end

.tandem_repeat ⇒ Object

Two or more adjcent copies of a region (of length greater than 1). (http://purl.obolibrary.org/obo/SO_0000705)

# File 'lib/biointerchange/so.rb', line 4553

def self.tandem_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000705')
end

.target_site_duplication ⇒ Object

A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion. (http://purl.obolibrary.org/obo/SO_0000434)

# File 'lib/biointerchange/so.rb', line 2919

def self.target_site_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000434')
end

.targeting_vector ⇒ Object

An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications. (http://purl.obolibrary.org/obo/SO_0001644)

# File 'lib/biointerchange/so.rb', line 10099

def self.targeting_vector
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001644')
end

.tasiRNA ⇒ Object

The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene. (http://purl.obolibrary.org/obo/SO_0001800)

# File 'lib/biointerchange/so.rb', line 11005

def self.tasiRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001800')
end

.tasiRNA_primary_transcript ⇒ Object

A primary transcript encoding a tasiRNA. (http://purl.obolibrary.org/obo/SO_0001801)

# File 'lib/biointerchange/so.rb', line 11011

def self.tasiRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001801')
end

.TATA_box ⇒ Object

A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T). (http://purl.obolibrary.org/obo/SO_0000174)

# File 'lib/biointerchange/so.rb', line 1361

def self.TATA_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000174')
end

.TCT_motif ⇒ Object

A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator. (http://purl.obolibrary.org/obo/SO_0001959)

# File 'lib/biointerchange/so.rb', line 11963

def self.TCT_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001959')
end

.telomerase_RNA ⇒ Object

The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA. (http://purl.obolibrary.org/obo/SO_0000390)

# File 'lib/biointerchange/so.rb', line 2655

def self.telomerase_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000390')
end

.telomerase_RNA_gene ⇒ Object

A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase. (http://purl.obolibrary.org/obo/SO_0001643)

# File 'lib/biointerchange/so.rb', line 10093

def self.telomerase_RNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001643')
end

.telomere ⇒ Object

A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end. (http://purl.obolibrary.org/obo/SO_0000624)

# File 'lib/biointerchange/so.rb', line 4067

def self.telomere
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000624')
end

.telomeric_repeat ⇒ Object

The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n. (http://purl.obolibrary.org/obo/SO_0001496)

# File 'lib/biointerchange/so.rb', line 9235

def self.telomeric_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001496')
end

.telomeric_transcript ⇒ Object

A non-coding transcript derived from thetranscript of the telomere. (http://purl.obolibrary.org/obo/SO_0001927)

# File 'lib/biointerchange/so.rb', line 11767

def self.telomeric_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001927')
end

.template_region ⇒ Object

A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA. (http://purl.obolibrary.org/obo/SO_0000978)

# File 'lib/biointerchange/so.rb', line 6143

def self.template_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000978')
end

.terminal_inverted_repeat ⇒ Object

An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon. (http://purl.obolibrary.org/obo/SO_0000481)

# File 'lib/biointerchange/so.rb', line 3205

def self.terminal_inverted_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000481')
end

.terminal_inverted_repeat_element ⇒ Object

A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long. (http://purl.obolibrary.org/obo/SO_0000208)

# File 'lib/biointerchange/so.rb', line 1569

def self.terminal_inverted_repeat_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000208')
end

.terminator ⇒ Object

The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. (http://purl.obolibrary.org/obo/SO_0000141)

# File 'lib/biointerchange/so.rb', line 1163

def self.terminator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000141')
end

.terminator_codon_variant ⇒ Object

A sequence variant whereby at least one of the bases in the terminator codon is changed. (http://purl.obolibrary.org/obo/SO_0001590)

# File 'lib/biointerchange/so.rb', line 9781

def self.terminator_codon_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001590')
end

.terminator_of_type_2_RNApol_III_promoter ⇒ Object

A terminator signal for RNA polymerase III transcription. (http://purl.obolibrary.org/obo/SO_0000615)

# File 'lib/biointerchange/so.rb', line 4013

def self.terminator_of_type_2_RNApol_III_promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000615')
end

.TERRA ⇒ Object

A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long. (http://purl.obolibrary.org/obo/SO_0001923)

# File 'lib/biointerchange/so.rb', line 11743

def self.TERRA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001923')
end

.tetraloop ⇒ Object

A base-paired stem with loop of 4 non-hydrogen bonded nucleotides. (http://purl.obolibrary.org/obo/SO_0001008)

# File 'lib/biointerchange/so.rb', line 6323

def self.tetraloop
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001008')
end

.tetranucleotide_repeat_microsatellite_feature ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000641)

# File 'lib/biointerchange/so.rb', line 4169

def self.tetranucleotide_repeat_microsatellite_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000641')
end

.TF_binding_site ⇒ Object

A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]. (http://purl.obolibrary.org/obo/SO_0000235)

# File 'lib/biointerchange/so.rb', line 1731

def self.TF_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000235')
end

.TF_binding_site_variant ⇒ Object

A sequence variant located within a transcription factor binding site. (http://purl.obolibrary.org/obo/SO_0001782)

# File 'lib/biointerchange/so.rb', line 10903

def self.TF_binding_site_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001782')
end

.TFBS_ablation ⇒ Object

A feature ablation whereby the deleted region includes a transcription factor binding site. (http://purl.obolibrary.org/obo/SO_0001895)

# File 'lib/biointerchange/so.rb', line 11575

def self.TFBS_ablation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001895')
end

.TFBS_amplification ⇒ Object

A feature amplification of a region containing a transcription factor binding site. (http://purl.obolibrary.org/obo/SO_0001892)

# File 'lib/biointerchange/so.rb', line 11557

def self.TFBS_amplification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001892')
end

.TFBS_fusion ⇒ Object

A fusion where the deletion brings together transcription factor binding sites. (http://purl.obolibrary.org/obo/SO_0001888)

# File 'lib/biointerchange/so.rb', line 11533

def self.TFBS_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001888')
end

.TFBS_translocation ⇒ Object

A feature translocation where the region contains a transcription factor binding site. (http://purl.obolibrary.org/obo/SO_0001885)

# File 'lib/biointerchange/so.rb', line 11515

def self.TFBS_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001885')
end

.theta_replication ⇒ Object

This has been obsoleted as it represents a process. replaced_by: GO:0070582 (http://purl.obolibrary.org/obo/SO_0000970)

# File 'lib/biointerchange/so.rb', line 6101

def self.theta_replication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000970')
end

.three_methylcytidine ⇒ Object

3-methylcytidine is a modified cytidine. (http://purl.obolibrary.org/obo/SO_0001281)

# File 'lib/biointerchange/so.rb', line 7951

def self.three_methylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001281')
end

.three_methylpseudouridine ⇒ Object

3_methylpseudouridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001377)

# File 'lib/biointerchange/so.rb', line 8527

def self.three_methylpseudouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001377')
end

.three_methyluridine ⇒ Object

3_methyluridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001372)

# File 'lib/biointerchange/so.rb', line 8497

def self.three_methyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001372')
end

.three_prime_cis_splice_site ⇒ Object

Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron. (http://purl.obolibrary.org/obo/SO_0000164)

# File 'lib/biointerchange/so.rb', line 1301

def self.three_prime_cis_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000164')
end

.three_prime_clip ⇒ Object

3'-most region of a precursor transcript that is clipped off during processing. (http://purl.obolibrary.org/obo/SO_0000557)

# File 'lib/biointerchange/so.rb', line 3665

def self.three_prime_clip
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000557')
end

.three_prime_coding_exon ⇒ Object

The coding exon that is most 3-prime on a given transcript. (http://purl.obolibrary.org/obo/SO_0000202)

# File 'lib/biointerchange/so.rb', line 1533

def self.three_prime_coding_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000202')
end

.three_prime_coding_exon_coding_region ⇒ Object

The sequence of the three_prime_coding_exon that codes for protein. (http://purl.obolibrary.org/obo/SO_0000197)

# File 'lib/biointerchange/so.rb', line 1503

def self.three_prime_coding_exon_coding_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000197')
end

.three_prime_coding_exon_noncoding_region ⇒ Object

The sequence of the 3' exon that is not coding. (http://purl.obolibrary.org/obo/SO_0000484)

# File 'lib/biointerchange/so.rb', line 3223

def self.three_prime_coding_exon_noncoding_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000484')
end

.three_prime_D_heptamer ⇒ Object

7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene. (http://purl.obolibrary.org/obo/SO_0000493)

# File 'lib/biointerchange/so.rb', line 3277

def self.three_prime_D_heptamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000493')
end

.three_prime_D_nonamer ⇒ Object

A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene. (http://purl.obolibrary.org/obo/SO_0000494)

# File 'lib/biointerchange/so.rb', line 3283

def self.three_prime_D_nonamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000494')
end

.three_prime_D_recombination_signal_sequence ⇒ Object

Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene. (http://purl.obolibrary.org/obo/SO_0000570)

# File 'lib/biointerchange/so.rb', line 3743

def self.three_prime_D_recombination_signal_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000570')
end

.three_prime_D_spacer ⇒ Object

A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS. (http://purl.obolibrary.org/obo/SO_0000495)

# File 'lib/biointerchange/so.rb', line 3289

def self.three_prime_D_spacer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000495')
end

.three_prime_EST ⇒ Object

An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs). (http://purl.obolibrary.org/obo/SO_0001209)

# File 'lib/biointerchange/so.rb', line 7525

def self.three_prime_EST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001209')
end

.three_prime_five_prime_overlap ⇒ Object

An attribute to describe a gene when the 3' region overlaps with another gene's 5' region. (http://purl.obolibrary.org/obo/SO_0000076)

# File 'lib/biointerchange/so.rb', line 773

def self.three_prime_five_prime_overlap
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000076')
end

.three_prime_flanking_region ⇒ Object

A flanking region located three prime of a specific region. (http://purl.obolibrary.org/obo/SO_0001417)

# File 'lib/biointerchange/so.rb', line 8767

def self.three_prime_flanking_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001417')
end

.three_prime_intron ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000192)

# File 'lib/biointerchange/so.rb', line 1473

def self.three_prime_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000192')
end

.three_prime_LTR ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000426)

# File 'lib/biointerchange/so.rb', line 2871

def self.three_prime_LTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000426')
end

.three_prime_LTR_component ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000849)

# File 'lib/biointerchange/so.rb', line 5375

def self.three_prime_LTR_component
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000849')
end

.three_prime_noncoding_exon ⇒ Object

Non-coding exon in the 3' UTR. (http://purl.obolibrary.org/obo/SO_0000444)

# File 'lib/biointerchange/so.rb', line 2983

def self.three_prime_noncoding_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000444')
end

.three_prime_RACE_clone ⇒ Object

A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host. (http://purl.obolibrary.org/obo/SO_0001433)

# File 'lib/biointerchange/so.rb', line 8857

def self.three_prime_RACE_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001433')
end

.three_prime_recoding_site ⇒ Object

The recoding stimulatory signal located downstream of the recoding site. (http://purl.obolibrary.org/obo/SO_1001277)

# File 'lib/biointerchange/so.rb', line 13601

def self.three_prime_recoding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001277')
end

.three_prime_repeat_recoding_signal ⇒ Object

A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements. (http://purl.obolibrary.org/obo/SO_1001286)

# File 'lib/biointerchange/so.rb', line 13649

def self.three_prime_repeat_recoding_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001286')
end

.three_prime_restriction_enzyme_junction ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001690)

# File 'lib/biointerchange/so.rb', line 10351

def self.three_prime_restriction_enzyme_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001690')
end

.three_prime_RST ⇒ Object

A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long. (http://purl.obolibrary.org/obo/SO_0001468)

# File 'lib/biointerchange/so.rb', line 9067

def self.three_prime_RST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001468')
end

.three_prime_stem_loop_structure ⇒ Object

A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region. (http://purl.obolibrary.org/obo/SO_1001279)

# File 'lib/biointerchange/so.rb', line 13607

def self.three_prime_stem_loop_structure
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001279')
end

.three_prime_sticky_end_restriction_enzyme_cleavage_site ⇒ Object

A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs. (http://purl.obolibrary.org/obo/SO_0001976)

# File 'lib/biointerchange/so.rb', line 12065

def self.three_prime_sticky_end_restriction_enzyme_cleavage_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001976')
end

.three_prime_terminal_inverted_repeat ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000421)

# File 'lib/biointerchange/so.rb', line 2841

def self.three_prime_terminal_inverted_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000421')
end

.three_prime_three_prime_overlap ⇒ Object

An attribute to describe a gene when the 3' region overlaps with another gene's 3' region. (http://purl.obolibrary.org/obo/SO_0000075)

# File 'lib/biointerchange/so.rb', line 767

def self.three_prime_three_prime_overlap
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000075')
end

.three_prime_UST ⇒ Object

A UST located in the 3'UTR of a protein-coding transcript. (http://purl.obolibrary.org/obo/SO_0001465)

# File 'lib/biointerchange/so.rb', line 9049

def self.three_prime_UST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001465')
end

.three_prime_UTR ⇒ Object

A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein. (http://purl.obolibrary.org/obo/SO_0000205)

# File 'lib/biointerchange/so.rb', line 1551

def self.three_prime_UTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000205')
end

.three_prime_UTR_intron ⇒ Object

An intron located in the 3' UTR. (http://purl.obolibrary.org/obo/SO_0000448)

# File 'lib/biointerchange/so.rb', line 3007

def self.three_prime_UTR_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000448')
end

.three_ten_helix ⇒ Object

The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier. (http://purl.obolibrary.org/obo/SO_0001119)

# File 'lib/biointerchange/so.rb', line 6985

def self.three_ten_helix
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001119')
end

.three_three_amino_three_carboxypropyl_uridine ⇒ Object

3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001353)

# File 'lib/biointerchange/so.rb', line 8383

def self.three_three_amino_three_carboxypropyl_uridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001353')
end

.three_two_prime_O_dimethyluridine ⇒ Object

3_2prime_O_dimethyluridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001375)

# File 'lib/biointerchange/so.rb', line 8515

def self.three_two_prime_O_dimethyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001375')
end

.threonine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001445)

# File 'lib/biointerchange/so.rb', line 8929

def self.threonine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001445')
end

.threonine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding threonyl tRNA (SO:000270). (http://purl.obolibrary.org/obo/SO_0000227)

# File 'lib/biointerchange/so.rb', line 1683

def self.threonine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000227')
end

.threonyl_tRNA ⇒ Object

A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region. (http://purl.obolibrary.org/obo/SO_0000270)

# File 'lib/biointerchange/so.rb', line 1941

def self.threonyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000270')
end

.tiling_path ⇒ Object

A set of regions which overlap with minimal polymorphism to form a linear sequence. (http://purl.obolibrary.org/obo/SO_0000472)

# File 'lib/biointerchange/so.rb', line 3151

def self.tiling_path
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000472')
end

.tiling_path_clone ⇒ Object

A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly. (http://purl.obolibrary.org/obo/SO_0000480)

# File 'lib/biointerchange/so.rb', line 3199

def self.tiling_path_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000480')
end

.tiling_path_fragment ⇒ Object

A piece of sequence that makes up a tiling_path (SO:0000472). (http://purl.obolibrary.org/obo/SO_0000474)

# File 'lib/biointerchange/so.rb', line 3163

def self.tiling_path_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000474')
end

.tmRNA ⇒ Object

A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes. (http://purl.obolibrary.org/obo/SO_0000584)

# File 'lib/biointerchange/so.rb', line 3827

def self.tmRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000584')
end

.tmRNA_acceptor_piece ⇒ Object

The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together. (http://purl.obolibrary.org/obo/SO_0000770)

# File 'lib/biointerchange/so.rb', line 4937

def self.tmRNA_acceptor_piece
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000770')
end

.tmRNA_coding_piece ⇒ Object

The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together. (http://purl.obolibrary.org/obo/SO_0000769)

# File 'lib/biointerchange/so.rb', line 4931

def self.tmRNA_coding_piece
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000769')
end

.tmRNA_encoding ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000659)

# File 'lib/biointerchange/so.rb', line 4277

def self.tmRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000659')
end

.tmRNA_gene ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001271)

# File 'lib/biointerchange/so.rb', line 7891

def self.tmRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001271')
end

.tmRNA_primary_transcript ⇒ Object

A primary transcript encoding a tmRNA (SO:0000584). (http://purl.obolibrary.org/obo/SO_0000586)

# File 'lib/biointerchange/so.rb', line 3839

def self.tmRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000586')
end

.tmRNA_region ⇒ Object

A region of a tmRNA. (http://purl.obolibrary.org/obo/SO_0000847)

# File 'lib/biointerchange/so.rb', line 5363

def self.tmRNA_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000847')
end

.TNA ⇒ Object

An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone. (http://purl.obolibrary.org/obo/SO_0001190)

# File 'lib/biointerchange/so.rb', line 7411

def self.TNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001190')
end

.TNA_oligo ⇒ Object

An oligo composed of TNA residues. (http://purl.obolibrary.org/obo/SO_0001191)

# File 'lib/biointerchange/so.rb', line 7417

def self.TNA_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001191')
end

.topologically_defined_region ⇒ Object

A region that is defined according to its relations with other regions within the same sequence. (http://purl.obolibrary.org/obo/SO_0001412)

# File 'lib/biointerchange/so.rb', line 8737

def self.topologically_defined_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001412')
end

.topology_attribute ⇒ Object

Attributes added to describe the different kinds of replicon. SO workshop, September 2006. (http://purl.obolibrary.org/obo/SO_0000986)

# File 'lib/biointerchange/so.rb', line 6191

def self.topology_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000986')
end

.TR_box ⇒ Object

A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis. (http://purl.obolibrary.org/obo/SO_0001858)

# File 'lib/biointerchange/so.rb', line 11353

def self.TR_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001858')
end

.trans_splice_acceptor_site ⇒ Object

The 3' splice site of the acceptor primary transcript. (http://purl.obolibrary.org/obo/SO_0000706)

# File 'lib/biointerchange/so.rb', line 4559

def self.trans_splice_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000706')
end

.trans_splice_donor_site ⇒ Object

The 5' five prime splice site region of the donor RNA. (http://purl.obolibrary.org/obo/SO_0000707)

# File 'lib/biointerchange/so.rb', line 4565

def self.trans_splice_donor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000707')
end

.trans_splice_junction ⇒ Object

The boundary between the spliced leader and the first exon of the mRNA. (http://purl.obolibrary.org/obo/SO_0001474)

# File 'lib/biointerchange/so.rb', line 9103

def self.trans_splice_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001474')
end

.trans_splice_site ⇒ Object

Primary transcript region bordering trans-splice junction. (http://purl.obolibrary.org/obo/SO_0001420)

# File 'lib/biointerchange/so.rb', line 8785

def self.trans_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001420')
end

.trans_spliced ⇒ Object

An attribute describing transcript sequence that is created by splicing exons from diferent genes. (http://purl.obolibrary.org/obo/SO_0000870)

# File 'lib/biointerchange/so.rb', line 5501

def self.trans_spliced
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000870')
end

.trans_spliced_from ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#trans_spliced_from)

# File 'lib/biointerchange/so.rb', line 269

def self.trans_spliced_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#trans_spliced_from')
end

.trans_spliced_mRNA ⇒ Object

An mRNA that is trans-spliced. (http://purl.obolibrary.org/obo/SO_0000872)

# File 'lib/biointerchange/so.rb', line 5513

def self.trans_spliced_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000872')
end

.trans_spliced_to ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/so_2_5_2.obo#trans_spliced_to)

# File 'lib/biointerchange/so.rb', line 275

def self.trans_spliced_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#trans_spliced_to')
end

.trans_spliced_transcript ⇒ Object

A transcript that is trans-spliced. (http://purl.obolibrary.org/obo/SO_0000479)

# File 'lib/biointerchange/so.rb', line 3193

def self.trans_spliced_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000479')
end

.transcribed_cluster ⇒ Object

A region defined by a set of transcribed sequences from the same gene or expressed pseudogene. (http://purl.obolibrary.org/obo/SO_0001457)

# File 'lib/biointerchange/so.rb', line 9001

def self.transcribed_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001457')
end

.transcribed_fragment ⇒ Object

An experimental region, defined by a tiling array experiment to be transcribed at some level. (http://purl.obolibrary.org/obo/SO_0001418)

# File 'lib/biointerchange/so.rb', line 8773

def self.transcribed_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001418')
end

.transcribed_from ⇒ Object

X is transcribed_from Y if X is synthesized from template Y. (http://purl.obolibrary.org/obo/so_2_5_2.obo#transcribed_from)

# File 'lib/biointerchange/so.rb', line 281

def self.transcribed_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#transcribed_from')
end

.transcribed_region ⇒ Object

A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes. (http://purl.obolibrary.org/obo/SO_0000502)

# File 'lib/biointerchange/so.rb', line 3331

def self.transcribed_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000502')
end

.transcribed_spacer_region ⇒ Object

Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA. (http://purl.obolibrary.org/obo/SO_0000638)

# File 'lib/biointerchange/so.rb', line 4151

def self.transcribed_spacer_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000638')
end

.transcribed_to ⇒ Object

Inverse of transcribed_from. (http://purl.obolibrary.org/obo/so_2_5_2.obo#transcribed_to)

# File 'lib/biointerchange/so.rb', line 287

def self.transcribed_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#transcribed_to')
end

.transcript ⇒ Object

An RNA synthesized on a DNA or RNA template by an RNA polymerase. (http://purl.obolibrary.org/obo/SO_0000673)

# File 'lib/biointerchange/so.rb', line 4361

def self.transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000673')
end

.transcript_ablation ⇒ Object

A feature ablation whereby the deleted region includes a transcript feature. (http://purl.obolibrary.org/obo/SO_0001893)

# File 'lib/biointerchange/so.rb', line 11563

def self.transcript_ablation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001893')
end

.transcript_amplification ⇒ Object

A feature amplification of a region containing a transcript. (http://purl.obolibrary.org/obo/SO_0001889)

# File 'lib/biointerchange/so.rb', line 11539

def self.transcript_amplification
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001889')
end

.transcript_attribute ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000237)

# File 'lib/biointerchange/so.rb', line 1743

def self.transcript_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000237')
end

.transcript_bound_by_nucleic_acid ⇒ Object

A transcript that is bound by a nucleic acid. (http://purl.obolibrary.org/obo/SO_0000278)

# File 'lib/biointerchange/so.rb', line 1989

def self.transcript_bound_by_nucleic_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000278')
end

.transcript_bound_by_protein ⇒ Object

A transcript that is bound by a protein. (http://purl.obolibrary.org/obo/SO_0000279)

# File 'lib/biointerchange/so.rb', line 1995

def self.transcript_bound_by_protein
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000279')
end

.transcript_edited_by_U_insertion_deletion ⇒ Object

The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa. (http://purl.obolibrary.org/obo/SO_0000597)

# File 'lib/biointerchange/so.rb', line 3905

def self.transcript_edited_by_U_insertion_deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000597')
end

.transcript_feature ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000115)

# File 'lib/biointerchange/so.rb', line 1007

def self.transcript_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000115')
end

.transcript_function_variant ⇒ Object

A sequence variant which alters the functioning of a transcript with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001538)

# File 'lib/biointerchange/so.rb', line 9487

def self.transcript_function_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001538')
end

.transcript_fusion ⇒ Object

A feature fusion where the deletion brings together transcript regions. (http://purl.obolibrary.org/obo/SO_0001886)

# File 'lib/biointerchange/so.rb', line 11521

def self.transcript_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001886')
end

.transcript_processing_variant ⇒ Object

A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001543)

# File 'lib/biointerchange/so.rb', line 9517

def self.transcript_processing_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001543')
end

.transcript_region ⇒ Object

A region of a transcript. (http://purl.obolibrary.org/obo/SO_0000833)

# File 'lib/biointerchange/so.rb', line 5279

def self.transcript_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000833')
end

.transcript_regulatory_region_fusion ⇒ Object

A feature fusion where the deletion brings together a regulatory region and a transcript region. (http://purl.obolibrary.org/obo/SO_0001890)

# File 'lib/biointerchange/so.rb', line 11545

def self.transcript_regulatory_region_fusion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001890')
end

.transcript_secondary_structure_variant ⇒ Object

A sequence variant within a transcript that changes the secondary structure of the RNA product. (http://purl.obolibrary.org/obo/SO_0001596)

# File 'lib/biointerchange/so.rb', line 9817

def self.transcript_secondary_structure_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001596')
end

.transcript_sequence_variant ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001579)

# File 'lib/biointerchange/so.rb', line 9733

def self.transcript_sequence_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001579')
end

.transcript_stability_variant ⇒ Object

A variant that changes the stability of a transcript with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001546)

# File 'lib/biointerchange/so.rb', line 9535

def self.transcript_stability_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001546')
end

.transcript_translocation ⇒ Object

A feature translocation where the region contains a transcript. (http://purl.obolibrary.org/obo/SO_0001883)

# File 'lib/biointerchange/so.rb', line 11503

def self.transcript_translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001883')
end

.transcript_variant ⇒ Object

A sequence variant that changes the structure of the transcript. (http://purl.obolibrary.org/obo/SO_0001576)

# File 'lib/biointerchange/so.rb', line 9715

def self.transcript_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001576')
end

.transcript_with_readthrough_stop_codon ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000117)

# File 'lib/biointerchange/so.rb', line 1019

def self.transcript_with_readthrough_stop_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000117')
end

.transcript_with_translational_frameshift ⇒ Object

A transcript with a translational frameshift. (http://purl.obolibrary.org/obo/SO_0000118)

# File 'lib/biointerchange/so.rb', line 1025

def self.transcript_with_translational_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000118')
end

.transcription_end_site ⇒ Object

The base where transcription ends. (http://purl.obolibrary.org/obo/SO_0000616)

# File 'lib/biointerchange/so.rb', line 4019

def self.transcription_end_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000616')
end

.transcription_regulatory_region ⇒ Object

A regulatory region that is involved in the control of the process of transcription. (http://purl.obolibrary.org/obo/SO_0001679)

# File 'lib/biointerchange/so.rb', line 10285

def self.transcription_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001679')
end

.transcription_start_cluster ⇒ Object

A region defined by a cluster of experimentally determined transcription starting sites. (http://purl.obolibrary.org/obo/SO_0001915)

# File 'lib/biointerchange/so.rb', line 11695

def self.transcription_start_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001915')
end

.transcription_variant ⇒ Object

A variant that changes alters the transcription of a transcript with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001549)

# File 'lib/biointerchange/so.rb', line 9553

def self.transcription_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001549')
end

.transcriptional_cis_regulatory_region ⇒ Object

A regulatory_region that modulates the transcription of a gene or genes. (http://purl.obolibrary.org/obo/SO_0001055)

# File 'lib/biointerchange/so.rb', line 6613

def self.transcriptional_cis_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001055')
end

.transcriptionally_constitutive ⇒ Object

Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate. (http://purl.obolibrary.org/obo/SO_0000124)

# File 'lib/biointerchange/so.rb', line 1061

def self.transcriptionally_constitutive
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000124')
end

.transcriptionally_induced ⇒ Object

An inducer molecule is required for transcription to occur. (http://purl.obolibrary.org/obo/SO_0000125)

# File 'lib/biointerchange/so.rb', line 1067

def self.transcriptionally_induced
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000125')
end

.transcriptionally_regulated ⇒ Object

An attribute describing a gene that is regulated at transcription. (http://purl.obolibrary.org/obo/SO_0000123)

# File 'lib/biointerchange/so.rb', line 1055

def self.transcriptionally_regulated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000123')
end

.transcriptionally_repressed ⇒ Object

A repressor molecule is required for transcription to stop. (http://purl.obolibrary.org/obo/SO_0000126)

# File 'lib/biointerchange/so.rb', line 1073

def self.transcriptionally_repressed
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000126')
end

.transgene ⇒ Object

A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another. (http://purl.obolibrary.org/obo/SO_0000902)

# File 'lib/biointerchange/so.rb', line 5693

def self.transgene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000902')
end

.transgene_attribute ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000452)

# File 'lib/biointerchange/so.rb', line 3031

def self.transgene_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000452')
end

.transgenic ⇒ Object

Attribute describing sequence that has been integrated with foreign sequence. (http://purl.obolibrary.org/obo/SO_0000781)

# File 'lib/biointerchange/so.rb', line 5003

def self.transgenic
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000781')
end

.transgenic_insertion ⇒ Object

An insertion that derives from another organism, via the use of recombinant DNA technology. (http://purl.obolibrary.org/obo/SO_0001218)

# File 'lib/biointerchange/so.rb', line 7579

def self.transgenic_insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001218')
end

.transgenic_transposable_element ⇒ Object

TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE. (http://purl.obolibrary.org/obo/SO_0000796)

# File 'lib/biointerchange/so.rb', line 5093

def self.transgenic_transposable_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000796')
end

.transit_peptide ⇒ Object

The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle). (http://purl.obolibrary.org/obo/SO_0000725)

# File 'lib/biointerchange/so.rb', line 4673

def self.transit_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000725')
end

.transition ⇒ Object

Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. (http://purl.obolibrary.org/obo/SO_1000009)

# File 'lib/biointerchange/so.rb', line 12497

def self.transition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000009')
end

.translated_nucleotide_match ⇒ Object

A match against a translated sequence. (http://purl.obolibrary.org/obo/SO_0000181)

# File 'lib/biointerchange/so.rb', line 1407

def self.translated_nucleotide_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000181')
end

.translates_to ⇒ Object

Inverse of translation _of. (http://purl.obolibrary.org/obo/so_2_5_2.obo#translates_to)

# File 'lib/biointerchange/so.rb', line 293

def self.translates_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#translates_to')
end

.translation_of ⇒ Object

X is translation of Y if Y is translated by ribosome to create X. (http://purl.obolibrary.org/obo/so_2_5_2.obo#translation_of)

# File 'lib/biointerchange/so.rb', line 299

def self.translation_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#translation_of')
end

.translation_regulatory_region ⇒ Object

A regulatory region that is involved in the control of the process of translation. (http://purl.obolibrary.org/obo/SO_0001680)

# File 'lib/biointerchange/so.rb', line 10291

def self.translation_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001680')
end

.translational_frameshift ⇒ Object

The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. (http://purl.obolibrary.org/obo/SO_0001210)

# File 'lib/biointerchange/so.rb', line 7531

def self.translational_frameshift
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001210')
end

.translational_product_function_variant ⇒ Object

A sequence variant that affects the functioning of a translational product with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001539)

# File 'lib/biointerchange/so.rb', line 9493

def self.translational_product_function_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001539')
end

.translational_product_level_variant ⇒ Object

A functional variant that changes the translational product level with respect to a reference sequence. (http://purl.obolibrary.org/obo/SO_0001553)

# File 'lib/biointerchange/so.rb', line 9577

def self.translational_product_level_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001553')
end

.translational_product_structure_variant ⇒ Object

A sequence variant within the transcript that changes the structure of the translational product. (http://purl.obolibrary.org/obo/SO_0001598)

# File 'lib/biointerchange/so.rb', line 9829

def self.translational_product_structure_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001598')
end

.translationally_frameshifted ⇒ Object

Recoding by frameshifting a particular site. (http://purl.obolibrary.org/obo/SO_0000887)

# File 'lib/biointerchange/so.rb', line 5603

def self.translationally_frameshifted
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000887')
end

.translationally_regulated ⇒ Object

An attribute describing a gene that is regulated as it is translated. (http://purl.obolibrary.org/obo/SO_0000131)

# File 'lib/biointerchange/so.rb', line 1103

def self.translationally_regulated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000131')
end

.translationally_regulated_gene ⇒ Object

A gene that is translationally regulated. (http://purl.obolibrary.org/obo/SO_0000896)

# File 'lib/biointerchange/so.rb', line 5657

def self.translationally_regulated_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000896')
end

.translocate ⇒ Object

To translocate a subsection of sequence. (http://purl.obolibrary.org/obo/SO_0000049)

# File 'lib/biointerchange/so.rb', line 603

def self.translocate
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000049')
end

.translocation ⇒ Object

A region of nucleotide sequence that has translocated to a new position. (http://purl.obolibrary.org/obo/SO_0000199)

# File 'lib/biointerchange/so.rb', line 1515

def self.translocation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000199')
end

.translocation_breakpoint ⇒ Object

The point within a chromosome where a translocation begins or ends. (http://purl.obolibrary.org/obo/SO_0001413)

# File 'lib/biointerchange/so.rb', line 8743

def self.translocation_breakpoint
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001413')
end

.translocation_element ⇒ Object

A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations. (http://purl.obolibrary.org/obo/SO_0000686)

# File 'lib/biointerchange/so.rb', line 4439

def self.translocation_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000686')
end

.translocaton_attribute ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001520)

# File 'lib/biointerchange/so.rb', line 9379

def self.translocaton_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001520')
end

.transmembrane_helix ⇒ Object

A region that traverses the lipid bilayer and adopts a helical secondary structure. (http://purl.obolibrary.org/obo/SO_0001812)

# File 'lib/biointerchange/so.rb', line 11077

def self.transmembrane_helix
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001812')
end

.transmembrane_polypeptide_region ⇒ Object

Polypeptide region traversing the lipid bilayer. (http://purl.obolibrary.org/obo/SO_0001077)

# File 'lib/biointerchange/so.rb', line 6733

def self.transmembrane_polypeptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001077')
end

.transposable_element ⇒ Object

A transposon or insertion sequence. An element that can insert in a variety of DNA sequences. (http://purl.obolibrary.org/obo/SO_0000101)

# File 'lib/biointerchange/so.rb', line 923

def self.transposable_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000101')
end

.transposable_element_attribute ⇒ Object

Added by KE Jan 2006 to capture the kinds of attributes of TEs (http://purl.obolibrary.org/obo/SO_0000780)

# File 'lib/biointerchange/so.rb', line 4997

def self.transposable_element_attribute
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000780')
end

.transposable_element_CDS ⇒ Object

A CDS that is part of a transposable element. (http://purl.obolibrary.org/obo/SO_0001896)

# File 'lib/biointerchange/so.rb', line 11581

def self.transposable_element_CDS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001896')
end

.transposable_element_flanking_region ⇒ Object

The region of sequence surrounding a transposable element. (http://purl.obolibrary.org/obo/SO_0000364)

# File 'lib/biointerchange/so.rb', line 2499

def self.transposable_element_flanking_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000364')
end

.transposable_element_gene ⇒ Object

A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast. (http://purl.obolibrary.org/obo/SO_0000111)

# File 'lib/biointerchange/so.rb', line 983

def self.transposable_element_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000111')
end

.transposable_element_insertion_site ⇒ Object

The junction in a genome where a transposable_element has inserted. (http://purl.obolibrary.org/obo/SO_0000368)

# File 'lib/biointerchange/so.rb', line 2523

def self.transposable_element_insertion_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000368')
end

.transposable_element_pseudogene ⇒ Object

A pseudogene contained within a transposable element. (http://purl.obolibrary.org/obo/SO_0001897)

# File 'lib/biointerchange/so.rb', line 11587

def self.transposable_element_pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001897')
end

.transposon_fragment ⇒ Object

A portion of a transposon, interrupted by the insertion of another element. (http://purl.obolibrary.org/obo/SO_0001054)

# File 'lib/biointerchange/so.rb', line 6607

def self.transposon_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001054')
end

.transversion ⇒ Object

Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. (http://purl.obolibrary.org/obo/SO_1000017)

# File 'lib/biointerchange/so.rb', line 12545

def self.transversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000017')
end

.trinucleotide_repeat_microsatellite_feature ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000291)

# File 'lib/biointerchange/so.rb', line 2067

def self.trinucleotide_repeat_microsatellite_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000291')
end

.tRNA ⇒ Object

Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position. (http://purl.obolibrary.org/obo/SO_0000253)

# File 'lib/biointerchange/so.rb', line 1839

def self.tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000253')
end

.tRNA_encoding ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000663)

# File 'lib/biointerchange/so.rb', line 4301

def self.tRNA_encoding
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000663')
end

.tRNA_gene ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001272)

# File 'lib/biointerchange/so.rb', line 7897

def self.tRNA_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001272')
end

.tRNA_intron ⇒ Object

An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification. (http://purl.obolibrary.org/obo/SO_1001272)

# File 'lib/biointerchange/so.rb', line 13577

def self.tRNA_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001272')
end

.tRNA_primary_transcript ⇒ Object

A primary transcript encoding a transfer RNA (SO:0000253). (http://purl.obolibrary.org/obo/SO_0000210)

# File 'lib/biointerchange/so.rb', line 1581

def self.tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000210')
end

.tRNA_region ⇒ Object

A region of a tRNA. (http://purl.obolibrary.org/obo/SO_0001172)

# File 'lib/biointerchange/so.rb', line 7303

def self.tRNA_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001172')
end

.tryptophan ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001440)

# File 'lib/biointerchange/so.rb', line 8899

def self.tryptophan
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001440')
end

.tryptophan_tRNA_primary_transcript ⇒ Object

A primary transcript encoding tryptophanyl tRNA (SO:000271). (http://purl.obolibrary.org/obo/SO_0000228)

# File 'lib/biointerchange/so.rb', line 1689

def self.tryptophan_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000228')
end

.tryptophanyl_tRNA ⇒ Object

A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region. (http://purl.obolibrary.org/obo/SO_0000271)

# File 'lib/biointerchange/so.rb', line 1947

def self.tryptophanyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000271')
end

.TSS ⇒ Object

The first base where RNA polymerase begins to synthesize the RNA transcript. (http://purl.obolibrary.org/obo/SO_0000315)

# File 'lib/biointerchange/so.rb', line 2211

def self.TSS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000315')
end

.TSS_region ⇒ Object

The region of a gene from the 5' most TSS to the 3' TSS. (http://purl.obolibrary.org/obo/SO_0001240)

# File 'lib/biointerchange/so.rb', line 7711

def self.TSS_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001240')
end

.twintron ⇒ Object

An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed. (http://purl.obolibrary.org/obo/SO_0000406)

# File 'lib/biointerchange/so.rb', line 2751

def self.twintron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000406')
end

.two_methyladenosine ⇒ Object

2_methyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001296)

# File 'lib/biointerchange/so.rb', line 8041

def self.two_methyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001296')
end

.two_methylthio_N6_cis_hydroxyisopentenyl_adenosine ⇒ Object

2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001303)

# File 'lib/biointerchange/so.rb', line 8083

def self.two_methylthio_N6_cis_hydroxyisopentenyl_adenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001303')
end

.two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine ⇒ Object

2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001309)

# File 'lib/biointerchange/so.rb', line 8119

def self.two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001309')
end

.two_methylthio_N6_isopentenyladenosine ⇒ Object

2_methylthio_N6_isopentenyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001301)

# File 'lib/biointerchange/so.rb', line 8071

def self.two_methylthio_N6_isopentenyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001301')
end

.two_methylthio_N6_methyladenosine ⇒ Object

2_methylthio_N6_methyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001299)

# File 'lib/biointerchange/so.rb', line 8059

def self.two_methylthio_N6_methyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001299')
end

.two_methylthio_N6_threonyl_carbamoyladenosine ⇒ Object

2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001306)

# File 'lib/biointerchange/so.rb', line 8101

def self.two_methylthio_N6_threonyl_carbamoyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001306')
end

.two_prime_O_methyladenosine ⇒ Object

2prime_O_methyladenosine is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001298)

# File 'lib/biointerchange/so.rb', line 8053

def self.two_prime_O_methyladenosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001298')
end

.two_prime_O_methylcytidine ⇒ Object

2'-O-methylcytidine is a modified cytidine. (http://purl.obolibrary.org/obo/SO_0001283)

# File 'lib/biointerchange/so.rb', line 7963

def self.two_prime_O_methylcytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001283')
end

.two_prime_O_methylguanosine ⇒ Object

2prime_O_methylguanosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001327)

# File 'lib/biointerchange/so.rb', line 8227

def self.two_prime_O_methylguanosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001327')
end

.two_prime_O_methylinosine ⇒ Object

2'-O-methylinosine is a modified inosine. (http://purl.obolibrary.org/obo/SO_0001280)

# File 'lib/biointerchange/so.rb', line 7945

def self.two_prime_O_methylinosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001280')
end

.two_prime_O_methylpseudouridine ⇒ Object

2prime_O_methylpseudouridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001348)

# File 'lib/biointerchange/so.rb', line 8353

def self.two_prime_O_methylpseudouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001348')
end

.two_prime_O_methyluridine ⇒ Object

2prime_O_methyluridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001345)

# File 'lib/biointerchange/so.rb', line 8335

def self.two_prime_O_methyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001345')
end

.two_prime_O_ribosyladenosine_phosphate ⇒ Object

2prime_O_ribosyladenosine_phosphate is a modified adenosine. (http://purl.obolibrary.org/obo/SO_0001310)

# File 'lib/biointerchange/so.rb', line 8125

def self.two_prime_O_ribosyladenosine_phosphate
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001310')
end

.two_prime_O_ribosylguanosine_phosphate ⇒ Object

2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001331)

# File 'lib/biointerchange/so.rb', line 8251

def self.two_prime_O_ribosylguanosine_phosphate
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001331')
end

.two_thio_two_prime_O_methyluridine ⇒ Object

2_thio_2prime_O_methyluridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001352)

# File 'lib/biointerchange/so.rb', line 8377

def self.two_thio_two_prime_O_methyluridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001352')
end

.two_thiocytidine ⇒ Object

2-thiocytidine is a modified cytidine. (http://purl.obolibrary.org/obo/SO_0001284)

# File 'lib/biointerchange/so.rb', line 7969

def self.two_thiocytidine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001284')
end

.two_thiouridine ⇒ Object

2_thiouridine is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001349)

# File 'lib/biointerchange/so.rb', line 8359

def self.two_thiouridine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001349')
end

.type_I_enzyme_restriction_site ⇒ Object

The recognition site is bipartite and interrupted. (http://purl.obolibrary.org/obo/SO_0000284)

# File 'lib/biointerchange/so.rb', line 2025

def self.type_I_enzyme_restriction_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000284')
end

.type_II_enzyme_restriction_site ⇒ Object

The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site. (http://purl.obolibrary.org/obo/SO_0000304)

# File 'lib/biointerchange/so.rb', line 2145

def self.type_II_enzyme_restriction_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000304')
end

.tyrosine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001446)

# File 'lib/biointerchange/so.rb', line 8935

def self.tyrosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001446')
end

.tyrosine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding tyrosyl tRNA (SO:000272). (http://purl.obolibrary.org/obo/SO_0000229)

# File 'lib/biointerchange/so.rb', line 1695

def self.tyrosine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000229')
end

.tyrosyl_tRNA ⇒ Object

A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region. (http://purl.obolibrary.org/obo/SO_0000272)

# File 'lib/biointerchange/so.rb', line 1953

def self.tyrosyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000272')
end

.U11_snRNA ⇒ Object

U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence. (http://purl.obolibrary.org/obo/SO_0000398)

# File 'lib/biointerchange/so.rb', line 2703

def self.U11_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000398')
end

.U12_intron ⇒ Object

A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs. (http://purl.obolibrary.org/obo/SO_0000295)

# File 'lib/biointerchange/so.rb', line 2091

def self.U12_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000295')
end

.U12_snRNA ⇒ Object

The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns. (http://purl.obolibrary.org/obo/SO_0000399)

# File 'lib/biointerchange/so.rb', line 2709

def self.U12_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000399')
end

.U14_snoRNA ⇒ Object

U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates. (http://purl.obolibrary.org/obo/SO_0000403)

# File 'lib/biointerchange/so.rb', line 2733

def self.U14_snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000403')
end

.U14_snoRNA_primary_transcript ⇒ Object

The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA. (http://purl.obolibrary.org/obo/SO_0005837)

# File 'lib/biointerchange/so.rb', line 12257

def self.U14_snoRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005837')
end

.U1_snRNA ⇒ Object

U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV. (http://purl.obolibrary.org/obo/SO_0000391)

# File 'lib/biointerchange/so.rb', line 2661

def self.U1_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000391')
end

.U2_intron ⇒ Object

A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs. (http://purl.obolibrary.org/obo/SO_0000184)

# File 'lib/biointerchange/so.rb', line 1425

def self.U2_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000184')
end

.U2_snRNA ⇒ Object

U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing. (http://purl.obolibrary.org/obo/SO_0000392)

# File 'lib/biointerchange/so.rb', line 2667

def self.U2_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000392')
end

.U3_five_prime_LTR_region ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000429)

# File 'lib/biointerchange/so.rb', line 2889

def self.U3_five_prime_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000429')
end

.U3_LTR_region ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000424)

# File 'lib/biointerchange/so.rb', line 2859

def self.U3_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000424')
end

.U3_snoRNA ⇒ Object

U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA. (http://purl.obolibrary.org/obo/SO_0001179)

# File 'lib/biointerchange/so.rb', line 7345

def self.U3_snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001179')
end

.U3_three_prime_LTR_region ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000431)

# File 'lib/biointerchange/so.rb', line 2901

def self.U3_three_prime_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000431')
end

.U4_snRNA ⇒ Object

U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6. (http://purl.obolibrary.org/obo/SO_0000393)

# File 'lib/biointerchange/so.rb', line 2673

def self.U4_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000393')
end

.U4atac_snRNA ⇒ Object

An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397). (http://purl.obolibrary.org/obo/SO_0000394)

# File 'lib/biointerchange/so.rb', line 2679

def self.U4atac_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000394')
end

.U5_five_prime_LTR_region ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000428)

# File 'lib/biointerchange/so.rb', line 2883

def self.U5_five_prime_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000428')
end

.U5_LTR_region ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000422)

# File 'lib/biointerchange/so.rb', line 2847

def self.U5_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000422')
end

.U5_snRNA ⇒ Object

U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation. (http://purl.obolibrary.org/obo/SO_0000395)

# File 'lib/biointerchange/so.rb', line 2685

def self.U5_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000395')
end

.U5_three_prime_LTR_region ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000432)

# File 'lib/biointerchange/so.rb', line 2907

def self.U5_three_prime_LTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000432')
end

.U6_snRNA ⇒ Object

U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA. (http://purl.obolibrary.org/obo/SO_0000396)

# File 'lib/biointerchange/so.rb', line 2691

def self.U6_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000396')
end

.U6atac_snRNA ⇒ Object

U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394). (http://purl.obolibrary.org/obo/SO_0000397)

# File 'lib/biointerchange/so.rb', line 2697

def self.U6atac_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000397')
end

.U_box ⇒ Object

An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription. (http://purl.obolibrary.org/obo/SO_0001788)

# File 'lib/biointerchange/so.rb', line 10933

def self.U_box
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001788')
end

.UAA_stop_codon_signal ⇒ Object

A stop codon signal for a UAA stop codon redefinition. (http://purl.obolibrary.org/obo/SO_1001283)

# File 'lib/biointerchange/so.rb', line 13631

def self.UAA_stop_codon_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001283')
end

.UAG_stop_codon_signal ⇒ Object

A stop codon signal for a UAG stop codon redefinition. (http://purl.obolibrary.org/obo/SO_1001282)

# File 'lib/biointerchange/so.rb', line 13625

def self.UAG_stop_codon_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001282')
end

.UGA_stop_codon_signal ⇒ Object

A stop codon signal for a UGA stop codon redefinition. (http://purl.obolibrary.org/obo/SO_1001285)

# File 'lib/biointerchange/so.rb', line 13643

def self.UGA_stop_codon_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001285')
end

.ultracontig ⇒ Object

An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers. (http://purl.obolibrary.org/obo/SO_0000719)

# File 'lib/biointerchange/so.rb', line 4637

def self.ultracontig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000719')
end

.unassigned_supercontig ⇒ Object

A supercontig that is not been assigned to any ultracontig during a genome assembly project. (http://purl.obolibrary.org/obo/SO_0001875)

# File 'lib/biointerchange/so.rb', line 11455

def self.unassigned_supercontig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001875')
end

.uncharacterised_chromosomal_mutation ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_1000170)

# File 'lib/biointerchange/so.rb', line 13313

def self.uncharacterised_chromosomal_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000170')
end

.undermodified_hydroxywybutosine ⇒ Object

Undermodified_hydroxywybutosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001335)

# File 'lib/biointerchange/so.rb', line 8275

def self.undermodified_hydroxywybutosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001335')
end

.unedited_region ⇒ Object

The region of an edited transcript that will not be edited. (http://purl.obolibrary.org/obo/SO_0000607)

# File 'lib/biointerchange/so.rb', line 3965

def self.unedited_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000607')
end

.unequally_crossed_over ⇒ Object

An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination. (http://purl.obolibrary.org/obo/SO_0000901)

# File 'lib/biointerchange/so.rb', line 5687

def self.unequally_crossed_over
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000901')
end

.unigene_cluster ⇒ Object

A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene. (http://purl.obolibrary.org/obo/SO_0001458)

# File 'lib/biointerchange/so.rb', line 9007

def self.unigene_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001458')
end

.uninverted_insertional_duplication ⇒ Object

An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments. (http://purl.obolibrary.org/obo/SO_1000152)

# File 'lib/biointerchange/so.rb', line 13247

def self.uninverted_insertional_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000152')
end

.uninverted_interchromosomal_transposition ⇒ Object

An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments. (http://purl.obolibrary.org/obo/SO_1000157)

# File 'lib/biointerchange/so.rb', line 13277

def self.uninverted_interchromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000157')
end

.uninverted_intrachromosomal_transposition ⇒ Object

An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments. (http://purl.obolibrary.org/obo/SO_1000159)

# File 'lib/biointerchange/so.rb', line 13289

def self.uninverted_intrachromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000159')
end

.unique_variant ⇒ Object

A physical quality which inheres to the variant by virtue of the number instances of the variant within a population. (http://purl.obolibrary.org/obo/SO_0001764)

# File 'lib/biointerchange/so.rb', line 10795

def self.unique_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001764')
end

.unitary_pseudogene ⇒ Object

A pseudogene, deactivated from original state by mutation, fixed in a population. (http://purl.obolibrary.org/obo/SO_0001759)

# File 'lib/biointerchange/so.rb', line 10765

def self.unitary_pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001759')
end

.unoriented_insertional_duplication ⇒ Object

An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded. (http://purl.obolibrary.org/obo/SO_1000160)

# File 'lib/biointerchange/so.rb', line 13295

def self.unoriented_insertional_duplication
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000160')
end

.unoriented_interchromosomal_transposition ⇒ Object

An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded. (http://purl.obolibrary.org/obo/SO_1000161)

# File 'lib/biointerchange/so.rb', line 13301

def self.unoriented_interchromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000161')
end

.unoriented_intrachromosomal_transposition ⇒ Object

An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded. (http://purl.obolibrary.org/obo/SO_1000162)

# File 'lib/biointerchange/so.rb', line 13307

def self.unoriented_intrachromosomal_transposition
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000162')
end

.untranslated_region_polycistronic_mRNA ⇒ Object

The untranslated sequence separating the 'cistrons' of multicistronic mRNA. (http://purl.obolibrary.org/obo/SO_0000242)

# File 'lib/biointerchange/so.rb', line 1773

def self.untranslated_region_polycistronic_mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000242')
end

.UPD ⇒ Object

Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent. (http://purl.obolibrary.org/obo/SO_0001744)

# File 'lib/biointerchange/so.rb', line 10675

def self.UPD
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001744')
end

.upstream_AUG_codon ⇒ Object

A start codon upstream of the ORF. (http://purl.obolibrary.org/obo/SO_0000630)

# File 'lib/biointerchange/so.rb', line 4103

def self.upstream_AUG_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000630')
end

.upstream_gene_variant ⇒ Object

A sequence variant located 5' of a gene. (http://purl.obolibrary.org/obo/SO_0001631)

# File 'lib/biointerchange/so.rb', line 10021

def self.upstream_gene_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001631')
end

.upstream_transcript_variant ⇒ Object

A feature variant, where the alteration occurs upstream of the transcript TSS. (http://purl.obolibrary.org/obo/SO_0001986)

# File 'lib/biointerchange/so.rb', line 12119

def self.upstream_transcript_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001986')
end

.uridine_five_oxyacetic_acid ⇒ Object

Uridine_5_oxyacetic_acid is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001356)

# File 'lib/biointerchange/so.rb', line 8401

def self.uridine_five_oxyacetic_acid
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001356')
end

.uridine_five_oxyacetic_acid_methyl_ester ⇒ Object

Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature. (http://purl.obolibrary.org/obo/SO_0001357)

# File 'lib/biointerchange/so.rb', line 8407

def self.uridine_five_oxyacetic_acid_methyl_ester
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001357')
end

.UST ⇒ Object

An EST spanning part or all of the untranslated regions of a protein-coding transcript. (http://purl.obolibrary.org/obo/SO_0001464)

# File 'lib/biointerchange/so.rb', line 9043

def self.UST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001464')
end

.UST_match ⇒ Object

A match against an UST sequence. (http://purl.obolibrary.org/obo/SO_0001470)

# File 'lib/biointerchange/so.rb', line 9079

def self.UST_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001470')
end

.UTR ⇒ Object

Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated. (http://purl.obolibrary.org/obo/SO_0000203)

# File 'lib/biointerchange/so.rb', line 1539

def self.UTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000203')
end

.UTR_intron ⇒ Object

Intron located in the untranslated region. (http://purl.obolibrary.org/obo/SO_0000446)

# File 'lib/biointerchange/so.rb', line 2995

def self.UTR_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000446')
end

.UTR_region ⇒ Object

A region of UTR. (http://purl.obolibrary.org/obo/SO_0000837)

# File 'lib/biointerchange/so.rb', line 5303

def self.UTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000837')
end

.UTR_variant ⇒ Object

A transcript variant that is located within the UTR. (http://purl.obolibrary.org/obo/SO_0001622)

# File 'lib/biointerchange/so.rb', line 9973

def self.UTR_variant
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001622')
end

.V_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene. (http://purl.obolibrary.org/obo/SO_0000526)

# File 'lib/biointerchange/so.rb', line 3475

def self.V_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000526')
end

.V_D_DJ_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000527)

# File 'lib/biointerchange/so.rb', line 3481

def self.V_D_DJ_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000527')
end

.V_D_DJ_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene. (http://purl.obolibrary.org/obo/SO_0000528)

# File 'lib/biointerchange/so.rb', line 3487

def self.V_D_DJ_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000528')
end

.V_D_DJ_J_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000529)

# File 'lib/biointerchange/so.rb', line 3493

def self.V_D_DJ_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000529')
end

.V_D_DJ_J_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene. (http://purl.obolibrary.org/obo/SO_0000530)

# File 'lib/biointerchange/so.rb', line 3499

def self.V_D_DJ_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000530')
end

.V_D_J_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000531)

# File 'lib/biointerchange/so.rb', line 3505

def self.V_D_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000531')
end

.V_D_J_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene. (http://purl.obolibrary.org/obo/SO_0000532)

# File 'lib/biointerchange/so.rb', line 3511

def self.V_D_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000532')
end

.V_DJ_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000542)

# File 'lib/biointerchange/so.rb', line 3571

def self.V_DJ_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000542')
end

.V_DJ_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene. (http://purl.obolibrary.org/obo/SO_0000518)

# File 'lib/biointerchange/so.rb', line 3427

def self.V_DJ_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000518')
end

.V_DJ_J_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000564)

# File 'lib/biointerchange/so.rb', line 3707

def self.V_DJ_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000564')
end

.V_DJ_J_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene. (http://purl.obolibrary.org/obo/SO_0000519)

# File 'lib/biointerchange/so.rb', line 3433

def self.V_DJ_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000519')
end

.V_gene_recombination_feature ⇒ Object

Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene. (http://purl.obolibrary.org/obo/SO_0000538)

# File 'lib/biointerchange/so.rb', line 3547

def self.V_gene_recombination_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000538')
end

.V_gene_segment ⇒ Object

Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR. (http://purl.obolibrary.org/obo/SO_0000466)

# File 'lib/biointerchange/so.rb', line 3115

def self.V_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000466')
end

.V_heptamer ⇒ Object

7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene. (http://purl.obolibrary.org/obo/SO_0000533)

# File 'lib/biointerchange/so.rb', line 3517

def self.V_heptamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000533')
end

.V_J_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000535)

# File 'lib/biointerchange/so.rb', line 3529

def self.V_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000535')
end

.V_J_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene. (http://purl.obolibrary.org/obo/SO_0000534)

# File 'lib/biointerchange/so.rb', line 3523

def self.V_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000534')
end

.V_nonamer ⇒ Object

9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene. (http://purl.obolibrary.org/obo/SO_0000536)

# File 'lib/biointerchange/so.rb', line 3535

def self.V_nonamer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000536')
end

.V_region ⇒ Object

The variable region of an immunoglobulin polypeptide sequence. (http://purl.obolibrary.org/obo/SO_0001833)

# File 'lib/biointerchange/so.rb', line 11203

def self.V_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001833')
end

.V_spacer ⇒ Object

12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene. (http://purl.obolibrary.org/obo/SO_0000537)

# File 'lib/biointerchange/so.rb', line 3541

def self.V_spacer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000537')
end

.V_VDJ_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000520)

# File 'lib/biointerchange/so.rb', line 3439

def self.V_VDJ_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000520')
end

.V_VDJ_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene. (http://purl.obolibrary.org/obo/SO_0000521)

# File 'lib/biointerchange/so.rb', line 3445

def self.V_VDJ_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000521')
end

.V_VDJ_J_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000565)

# File 'lib/biointerchange/so.rb', line 3713

def self.V_VDJ_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000565')
end

.V_VDJ_J_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene. (http://purl.obolibrary.org/obo/SO_0000522)

# File 'lib/biointerchange/so.rb', line 3451

def self.V_VDJ_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000522')
end

.V_VJ_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000523)

# File 'lib/biointerchange/so.rb', line 3457

def self.V_VJ_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000523')
end

.V_VJ_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene. (http://purl.obolibrary.org/obo/SO_0000524)

# File 'lib/biointerchange/so.rb', line 3463

def self.V_VJ_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000524')
end

.V_VJ_J_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000566)

# File 'lib/biointerchange/so.rb', line 3719

def self.V_VJ_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000566')
end

.V_VJ_J_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene. (http://purl.obolibrary.org/obo/SO_0000525)

# File 'lib/biointerchange/so.rb', line 3469

def self.V_VJ_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000525')
end

.vacuolar_sorting_signal ⇒ Object

A polypeptide region that targets a polypeptide to the vacuole. (http://purl.obolibrary.org/obo/SO_0001813)

# File 'lib/biointerchange/so.rb', line 11083

def self.vacuolar_sorting_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001813')
end

.validated ⇒ Object

An attribute to describe a feature that has been proven. (http://purl.obolibrary.org/obo/SO_0000789)

# File 'lib/biointerchange/so.rb', line 5051

def self.validated
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000789')
end

.validated_cDNA_clone ⇒ Object

A cDNA clone that has been validated. (http://purl.obolibrary.org/obo/SO_0000808)

# File 'lib/biointerchange/so.rb', line 5141

def self.validated_cDNA_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000808')
end

.valine ⇒ Object

A place holder for a cross product with chebi. (http://purl.obolibrary.org/obo/SO_0001436)

# File 'lib/biointerchange/so.rb', line 8875

def self.valine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001436')
end

.valine_tRNA_primary_transcript ⇒ Object

A primary transcript encoding valyl tRNA (SO:000273). (http://purl.obolibrary.org/obo/SO_0000230)

# File 'lib/biointerchange/so.rb', line 1701

def self.valine_tRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000230')
end

.valyl_tRNA ⇒ Object

A tRNA sequence that has a valine anticodon, and a 3' valine binding region. (http://purl.obolibrary.org/obo/SO_0000273)

# File 'lib/biointerchange/so.rb', line 1959

def self.valyl_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000273')
end

.variant_collection ⇒ Object

A collection of one or more sequences of an individual. (http://purl.obolibrary.org/obo/SO_0001507)

# File 'lib/biointerchange/so.rb', line 9301

def self.variant_collection
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001507')
end

.variant_frequency ⇒ Object

A physical quality which inheres to the variant by virtue of the number instances of the variant within a population. (http://purl.obolibrary.org/obo/SO_0001763)

# File 'lib/biointerchange/so.rb', line 10789

def self.variant_frequency
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001763')
end

.variant_genome ⇒ Object

A collection of sequences (often chromosomes) of an individual. (http://purl.obolibrary.org/obo/SO_0001506)

# File 'lib/biointerchange/so.rb', line 9295

def self.variant_genome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001506')
end

.variant_of ⇒ Object

Either:

A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
(http://purl.obolibrary.org/obo/so_2_5_2.obo#variant_of)

Or:

A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
(http://purl.obolibrary.org/obo/anonymous#variant_of)

# File 'lib/biointerchange/so.rb', line 309

def self.variant_of
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/so_2_5_2.obo#variant_of'), RDF::URI.new('http://purl.obolibrary.org/obo/anonymous#variant_of') ]
end

.variant_origin ⇒ Object

A quality inhering in a variant by virtue of its origin. (http://purl.obolibrary.org/obo/SO_0001762)

# File 'lib/biointerchange/so.rb', line 10783

def self.variant_origin
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001762')
end

.variant_phenotype ⇒ Object

A quality inhering in a variant by virtue of its phenotype. (http://purl.obolibrary.org/obo/SO_0001769)

# File 'lib/biointerchange/so.rb', line 10825

def self.variant_phenotype
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001769')
end

.variant_quality ⇒ Object

A dependent entity that inheres in a bearer, a sequence variant. (http://purl.obolibrary.org/obo/SO_0001761)

# File 'lib/biointerchange/so.rb', line 10777

def self.variant_quality
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001761')
end

.vault_RNA ⇒ Object

A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance. (http://purl.obolibrary.org/obo/SO_0000404)

# File 'lib/biointerchange/so.rb', line 2739

def self.vault_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000404')
end

.VD_gene_segment ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205). (http://purl.obolibrary.org/obo/SO_0000510)

# File 'lib/biointerchange/so.rb', line 3379

def self.VD_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000510')
end

.VDJ_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000541)

# File 'lib/biointerchange/so.rb', line 3565

def self.VDJ_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000541')
end

.VDJ_gene_segment ⇒ Object

Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205). (http://purl.obolibrary.org/obo/SO_0000574)

# File 'lib/biointerchange/so.rb', line 3767

def self.VDJ_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000574')
end

.VDJ_J_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000487)

# File 'lib/biointerchange/so.rb', line 3241

def self.VDJ_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000487')
end

.VDJ_J_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene. (http://purl.obolibrary.org/obo/SO_0000488)

# File 'lib/biointerchange/so.rb', line 3247

def self.VDJ_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000488')
end

.vector_replicon ⇒ Object

A replicon that has been modified to act as a vector for foreign sequence. (http://purl.obolibrary.org/obo/SO_0000440)

# File 'lib/biointerchange/so.rb', line 2959

def self.vector_replicon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000440')
end

.vertebrate_immune_system_feature ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000937)

# File 'lib/biointerchange/so.rb', line 5903

def self.vertebrate_immune_system_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000937')
end

.vertebrate_immune_system_gene_recombination_feature ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000301)

# File 'lib/biointerchange/so.rb', line 2127

def self.vertebrate_immune_system_gene_recombination_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000301')
end

.vertebrate_immune_system_gene_recombination_signal_feature ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000939)

# File 'lib/biointerchange/so.rb', line 5915

def self.vertebrate_immune_system_gene_recombination_signal_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000939')
end

.vertebrate_immune_system_gene_recombination_spacer ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000563)

# File 'lib/biointerchange/so.rb', line 3701

def self.vertebrate_immune_system_gene_recombination_spacer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000563')
end

.vertebrate_immunoglobulin_T_cell_receptor_gene_cluster ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000482)

# File 'lib/biointerchange/so.rb', line 3211

def self.vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000482')
end

.vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000938)

# File 'lib/biointerchange/so.rb', line 5909

def self.vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000938')
end

.vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000936)

# File 'lib/biointerchange/so.rb', line 5897

def self.vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000936')
end

.vertebrate_immunoglobulin_T_cell_receptor_segment ⇒ Object

I am using the term segment instead of gene here to avoid confusion with the region 'gene'. (http://purl.obolibrary.org/obo/SO_0000460)

# File 'lib/biointerchange/so.rb', line 3079

def self.vertebrate_immunoglobulin_T_cell_receptor_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000460')
end

.viral_sequence ⇒ Object

The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell. (http://purl.obolibrary.org/obo/SO_0001041)

# File 'lib/biointerchange/so.rb', line 6521

def self.viral_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001041')
end

.virtual_sequence ⇒ Object

A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database. (http://purl.obolibrary.org/obo/SO_0000499)

# File 'lib/biointerchange/so.rb', line 3313

def self.virtual_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000499')
end

.VJ_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000489)

# File 'lib/biointerchange/so.rb', line 3253

def self.VJ_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000489')
end

.VJ_gene_segment ⇒ Object

Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205). (http://purl.obolibrary.org/obo/SO_0000576)

# File 'lib/biointerchange/so.rb', line 3779

def self.VJ_gene_segment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000576')
end

.VJ_J_C_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene. (http://purl.obolibrary.org/obo/SO_0000490)

# File 'lib/biointerchange/so.rb', line 3259

def self.VJ_J_C_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000490')
end

.VJ_J_cluster ⇒ Object

Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene. (http://purl.obolibrary.org/obo/SO_0000491)

# File 'lib/biointerchange/so.rb', line 3265

def self.VJ_J_cluster
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000491')
end

.W_region ⇒ Object

The leftmost segment of homology in the HML and MAT mating loci, but not present in HMR. (http://purl.obolibrary.org/obo/SO_0002000)

# File 'lib/biointerchange/so.rb', line 12203

def self.W_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002000')
end

.WC_base_pair ⇒ Object

The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation. (http://purl.obolibrary.org/obo/SO_0000029)

# File 'lib/biointerchange/so.rb', line 483

def self.WC_base_pair
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000029')
end

.whole_genome_sequence_status ⇒ Object

The status of whole genome sequence. (http://purl.obolibrary.org/obo/SO_0001499)

# File 'lib/biointerchange/so.rb', line 9253

def self.whole_genome_sequence_status
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001499')
end

.wild_type ⇒ Object

An attribute describing sequence with the genotype found in nature and/or standard laboratory stock. (http://purl.obolibrary.org/obo/SO_0000817)

# File 'lib/biointerchange/so.rb', line 5195

def self.wild_type
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000817')
end

.wild_type_rescue_gene ⇒ Object

A gene that rescues. (http://purl.obolibrary.org/obo/SO_0000818)

# File 'lib/biointerchange/so.rb', line 5201

def self.wild_type_rescue_gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000818')
end

.with_parent(uris, parent) ⇒ Object

Returns only those URIs that fall under a designated parent URI.

uris

Set of URIs that are tested whether they have the given parent URI.

parent

Parent URI.

# File 'lib/biointerchange/so.rb', line 20555

def self.with_parent(uris, parent)
  return uris.select { |uri| has_parent?(uri, parent) }
end

.wobble_base_pair ⇒ Object

A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C. (http://purl.obolibrary.org/obo/SO_0001015)

# File 'lib/biointerchange/so.rb', line 6365

def self.wobble_base_pair
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001015')
end

.wybutosine ⇒ Object

Wybutosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001332)

# File 'lib/biointerchange/so.rb', line 8257

def self.wybutosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001332')
end

.wyosine ⇒ Object

Wyosine is a modified guanosine base feature. (http://purl.obolibrary.org/obo/SO_0001336)

# File 'lib/biointerchange/so.rb', line 8281

def self.wyosine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001336')
end

.X_element ⇒ Object

The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site. (http://purl.obolibrary.org/obo/SO_0001497)

# File 'lib/biointerchange/so.rb', line 9241

def self.X_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001497')
end

.X_element_combinatorial_repeat ⇒ Object

An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element. (http://purl.obolibrary.org/obo/SO_0001484)

# File 'lib/biointerchange/so.rb', line 9163

def self.X_element_combinatorial_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001484')
end

.Y_prime_element ⇒ Object

A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies. (http://purl.obolibrary.org/obo/SO_0001485)

# File 'lib/biointerchange/so.rb', line 9169

def self.Y_prime_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001485')
end

.Y_region ⇒ Object

A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha). (http://purl.obolibrary.org/obo/SO_0002001)

# File 'lib/biointerchange/so.rb', line 12209

def self.Y_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002001')
end

.Y_RNA ⇒ Object

Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin. (http://purl.obolibrary.org/obo/SO_0000405)

# File 'lib/biointerchange/so.rb', line 2745

def self.Y_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000405')
end

.YAC ⇒ Object

Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells. (http://purl.obolibrary.org/obo/SO_0000152)

# File 'lib/biointerchange/so.rb', line 1229

def self.YAC
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000152')
end

.YAC_clone ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0000760)

# File 'lib/biointerchange/so.rb', line 4883

def self.YAC_clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000760')
end

.YAC_end ⇒ Object

A region of sequence from the end of a YAC clone that may provide a highly specific marker. (http://purl.obolibrary.org/obo/SO_0001498)

# File 'lib/biointerchange/so.rb', line 9247

def self.YAC_end
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001498')
end

.Z1_region ⇒ Object

A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR). (http://purl.obolibrary.org/obo/SO_0002002)

# File 'lib/biointerchange/so.rb', line 12215

def self.Z1_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002002')
end

.Z2_region ⇒ Object

A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR). (http://purl.obolibrary.org/obo/SO_0002003)

# File 'lib/biointerchange/so.rb', line 12221

def self.Z2_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002003')
end

.zinc_finger_binding_site ⇒ Object

-- No comment or description provided. -- (http://purl.obolibrary.org/obo/SO_0001971)

# File 'lib/biointerchange/so.rb', line 12035

def self.zinc_finger_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001971')
end

.zinc_repressed_element ⇒ Object

A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc. (http://purl.obolibrary.org/obo/SO_0002006)

# File 'lib/biointerchange/so.rb', line 12239

def self.zinc_repressed_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0002006')
end