Class: BioInterchange::SOFA

Inherits:

Object

Object
BioInterchange::SOFA

show all

Defined in:: lib/biointerchange/sofa.rb

Class Method Summary collapse

.adjacent_to ⇒ Object

A geometric operator, specified in Egenhofer 1989.
.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.
.ARS ⇒ Object

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

This relationship is vague and up for discussion.
.attenuator ⇒ Object

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

A self spliced intron.
.base ⇒ Object

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

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

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

A structure consisting of a 7-methylguanosine in 5’-5’ triphosphate linkage with the first nucleotide of an mRNA.
.cDNA_match ⇒ Object

A match against cDNA sequence.
.CDS ⇒ Object

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

A region of a CDS.
.centromere ⇒ Object

A region of chromosome where the spindle fibers attach during mitosis and meiosis.
.chromosomal_structural_element ⇒ 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_band ⇒ Object

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

A region of a chromosome.
.cis_splice_site ⇒ Object

Intronic 2 bp region bordering exon.
.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_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

The start of the clone insert.
.coding_conserved_region ⇒ Object

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

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

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

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

A non-functional descendant of an exon.
.deletion ⇒ Object

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

A repeat where the same sequence is repeated in the same direction.
.disconnected_from ⇒ Object

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

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

A double stranded oligonucleotide.
.edited_from ⇒ Object

– No comment or description provided.
.edited_to ⇒ 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.
.enzymatic_RNA ⇒ Object

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

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

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

A region of an exon.
.experimental_feature ⇒ Object

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

A region of sequence implicated in an experimental result.
.expressed_sequence_match ⇒ Object

A match to an EST or cDNA sequence.
.finished_by ⇒ Object

Xy is finished_by Y if Y part of X, and X and Y share a 3’ boundary.
.finishes ⇒ Object

X finishes Y if X is part_of Y and X and Y share a 3’ or C terminal boundary.
.five_prime_cis_splice_site ⇒ Object

Intronic 2 bp region bordering the exon, at the 5’ edge of the intron.
.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_UTR ⇒ Object

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

The sequences extending on either side of a specific region.
.gained ⇒ Object

X gained Y if X is a variant_of X’ and Y part of X but not X’.
.gap ⇒ Object

A gap in the sequence of known length.
.gene ⇒ Object

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

– No comment or description provided.
.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_part ⇒ Object

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

– No comment or description provided.
.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.
.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.
.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.
.guided_by ⇒ Object

– No comment or description provided.
.guides ⇒ Object

– No comment or description provided.
.hammerhead_ribozyme ⇒ Object

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

– No comment or description provided.
.immature_peptide_region ⇒ Object

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

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

The junction where an insertion occurred.
.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.
.integral_part_of ⇒ Object

X integral_part_of Y if and only if: X part_of Y and Y has_part X.
.integrated_mobile_genetic_element ⇒ Object

An MGE that is integrated into the host chromosome.
.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.
.interior_coding_exon ⇒ 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.
.inversion ⇒ Object

A continuous nucleotide sequence is inverted in the same position.
.inverted_repeat ⇒ Object

The sequence is complementarily repeated on the opposite strand.
.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.
.junction ⇒ Object

A sequence_feature with an extent of zero.
.kozak_sequence ⇒ Object

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

Ribosomal RNA transcript that structures the large subunit of the ribosome.
.lost ⇒ Object

X lost Y if X is a variant_of X’ and Y part of X’ but not X.
.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.
.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.
.maximally_overlaps ⇒ Object

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

A subtype of part_of.
.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.
.microsatellite ⇒ Object

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

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

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

A modified nucleotide, i.e.
.mRNA ⇒ Object

Messenger RNA is the intermediate molecule between DNA and protein.
.mRNA_region ⇒ Object

A region of an mRNA.
.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.
.non_functional_homolog_of ⇒ Object

A relationship between a pseudogenic feature and its functional ancestor.
.non_transcribed_region ⇒ Object

A region of the gene which is not transcribed.
.noncoding_exon ⇒ Object

An exon that does not contain any codons.
.noncoding_region_of_exon ⇒ Object

The maximal intersection of exon and UTR.
.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_sensitive_site ⇒ Object

A region of nucleotide sequence targeted by a nuclease enzyme.
.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.
.oligo ⇒ Object

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

– No comment or description provided.
.overlaps ⇒ Object

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

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

A region amplified by a PCR reaction.
.peptide_localization_signal ⇒ Object

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

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

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

The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
.position_of ⇒ Object

– No comment or description provided.
.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.
.primary_transcript ⇒ Object

A transcript that in its initial state requires modification to be functional.
.primary_transcript_region ⇒ Object

A part of a primary transcript.
.primer ⇒ Object

An oligo to which new deoxyribonucleotides can be added by DNA polymerase.
.processed_from ⇒ Object

Inverse of processed_into.
.processed_into ⇒ Object

X is processed_into Y if a region X is modified to create Y.
.promoter ⇒ Object

A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.
.protein_binding_site ⇒ Object

A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
.protein_coding_primary_transcript ⇒ Object

A primary transcript that, at least in part, encodes one or more proteins.
.protein_match ⇒ Object

A match against a protein sequence.
.proviral_region ⇒ Object

A viral sequence which has integrated into a host genome.
.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).
.pseudogenic_region ⇒ Object

A non-functional descendent of a functional entity.
.pseudogenic_rRNA ⇒ Object

A non functional descendent of an rRNA.
.pseudogenic_tRNA ⇒ Object

A non functional descendent of a tRNA.
.rasiRNA ⇒ Object

A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
.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.
.recombined_from ⇒ Object

– No comment or description provided.
.recombined_to ⇒ Object

– No comment or description provided.
.region ⇒ Object

A sequence_feature with an extent greater than zero.
.regulatory_region ⇒ Object

A region of sequence that is involved in the control of a biological process.
.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_family ⇒ Object

A group of characterized repeat sequences.
.repeat_region ⇒ Object

A region of sequence containing one or more repeat units.
.replicon ⇒ Object

A region containing at least one unique origin of replication and a unique termination site.
.restriction_fragment ⇒ Object

A region of polynucleotide sequence produced by digestion with a restriction endonuclease.
.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.
.ribosome_entry_site ⇒ Object

Region in mRNA where ribosome assembles.
.ribozyme ⇒ Object

An RNA with catalytic activity.
.RNA_motif ⇒ Object

A motif that is active in RNA sequence.
.RNAi_reagent ⇒ Object

A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.
.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_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.
.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_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_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.
.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.
.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.
.scRNA ⇒ Object

A small non coding RNA sequence, present in the cytoplasm.
.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_difference ⇒ Object

A region where the sequence differs from that of a specified sequence.
.sequence_feature ⇒ Object

Any extent of continuous biological sequence.
.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_variant_obs ⇒ Object

A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
.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.
.silencer ⇒ Object

A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.
.similar_to ⇒ Object

– No comment or description provided.
.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.
.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.
.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.
.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.
.SNV ⇒ Object

SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.
.splice_enhancer ⇒ Object

Region of a transcript that regulates splicing.
.splice_site ⇒ Object

Consensus region of primary transcript bordering junction of splicing.
.spliceosomal_intron ⇒ Object

An intron which is spliced by the spliceosome.
.spliceosomal_intron_region ⇒ Object

A region within an intron.
.splicing_regulatory_region ⇒ Object

A regulatory_region that modulates splicing.
.SRP_RNA ⇒ Object

The signal recognition particle (SRP) is a universally conserved ribonucleoprotein.
.ss_oligo ⇒ Object

A single stranded oligonucleotide.
.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.
.stop_codon ⇒ Object

In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.
.stRNA ⇒ Object

Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C.
.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.
.substitution ⇒ Object

A sequence alteration where the length of the change in the variant is the same as that of the reference.
.supercontig ⇒ Object

One or more contigs that have been ordered and oriented using end-read information.
.tag ⇒ Object

A nucleotide sequence that may be used to identify a larger sequence.
.tandem_repeat ⇒ Object

Two or more adjcent copies of a region (of length greater than 1).
.telomerase_RNA ⇒ Object

The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.
.telomere ⇒ Object

A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.
.terminator ⇒ Object

The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
.TF_binding_site ⇒ Object

A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667].
.three_prime_cis_splice_site ⇒ Object

Intronic 2 bp region bordering the exon, at the 3’ edge of the intron.
.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_UTR ⇒ Object

A region at the 3’ end of a mature transcript (following the stop codon) that is not translated into a protein.
.tiling_path ⇒ Object

A set of regions which overlap with minimal polymorphism to form a linear sequence.
.tiling_path_fragment ⇒ Object

A piece of sequence that makes up a tiling_path (SO:0000472).
.topologically_defined_region ⇒ Object

A region that is defined according to its relations with other regions within the same sequence.
.trans_splice_acceptor_site ⇒ Object

The 3’ splice site of the acceptor primary transcript.
.trans_splice_site ⇒ Object

Primary transcript region bordering trans-splice junction.
.trans_spliced_from ⇒ Object

– No comment or description provided.
.trans_spliced_to ⇒ Object

– No comment or description provided.
.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_to ⇒ Object

Inverse of transcribed_from.
.transcript ⇒ Object

An RNA synthesized on a DNA or RNA template by an RNA polymerase.
.transcript_region ⇒ Object

A region of a transcript.
.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.
.transcriptional_cis_regulatory_region ⇒ Object

A regulatory_region that modulates the transcription of a gene or genes.
.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).
.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.
.transposable_element ⇒ Object

A transposon or insertion sequence.
.transposable_element_insertion_site ⇒ Object

The junction in a genome where a transposable_element has inserted.
.tRNA ⇒ Object

Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length.
.TSS ⇒ Object

The first base where RNA polymerase begins to synthesize the RNA transcript.
.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_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.
.U1_snRNA ⇒ Object

U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing).
.U2_snRNA ⇒ Object

U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing).
.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_snRNA ⇒ Object

U5 RNA is a component of both types of known spliceosome.
.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.
.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.
.UTR ⇒ Object

Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
.UTR_region ⇒ Object

A region of UTR.
.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.
.vault_RNA ⇒ Object

A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex.
.virtual_sequence ⇒ Object

A continuous piece of sequence similar to the ‘virtual contig’ concept of the Ensembl database.
.with_parent(uris, parent) ⇒ Object

Returns only those URIs that fall under a designated parent URI.
.Y_RNA ⇒ Object

Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins.

Class Method Details

.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. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#adjacent_to)



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# File 'lib/biointerchange/sofa.rb', line 17

def self.adjacent_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#adjacent_to')
end

.antisense_primary_transcript ⇒ `Object`

The reverse complement of the primary transcript. (purl.obolibrary.org/obo/SO_0000645)



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# File 'lib/biointerchange/sofa.rb', line 1281

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. (purl.obolibrary.org/obo/SO_0000644)



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# File 'lib/biointerchange/sofa.rb', line 1275

def self.antisense_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000644')
end

.ARS ⇒ `Object`

A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host. (purl.obolibrary.org/obo/SO_0000436)



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# File 'lib/biointerchange/sofa.rb', line 1071

def self.ARS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000436')
end

.assembly ⇒ `Object`

A region of the genome of known length that is composed by ordering and aligning two or more different regions. (purl.obolibrary.org/obo/SO_0001248)



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# File 'lib/biointerchange/sofa.rb', line 1683

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. (purl.obolibrary.org/obo/SO_0000143)



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# File 'lib/biointerchange/sofa.rb', line 465

def self.assembly_component
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000143')
end

.associated_with ⇒ `Object`

This relationship is vague and up for discussion. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#associated_with)



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# File 'lib/biointerchange/sofa.rb', line 23

def self.associated_with
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#associated_with')
end

.attenuator ⇒ `Object`

A sequence segment located within the five prime end of an mRNA that causes premature termination of translation. (purl.obolibrary.org/obo/SO_0000140)



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# File 'lib/biointerchange/sofa.rb', line 453

def self.attenuator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000140')
end

.autocatalytically_spliced_intron ⇒ `Object`

A self spliced intron. (purl.obolibrary.org/obo/SO_0000588)



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# File 'lib/biointerchange/sofa.rb', line 1185

def self.autocatalytically_spliced_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000588')
end

.base ⇒ `Object`

A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. (purl.obolibrary.org/obo/SO_0001236)



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# File 'lib/biointerchange/sofa.rb', line 1677

def self.base
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001236')
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. (purl.obolibrary.org/obo/SO_0000409)



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# File 'lib/biointerchange/sofa.rb', line 1035

def self.binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000409')
end

.biological_region ⇒ `Object`

A region defined by its disposition to be involved in a biological process. (purl.obolibrary.org/obo/SO_0001411)



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# File 'lib/biointerchange/sofa.rb', line 1701

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. (purl.obolibrary.org/obo/SO_0001409)



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# File 'lib/biointerchange/sofa.rb', line 1689

def self.biomaterial_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001409')
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. (purl.obolibrary.org/obo/SO_0000611)



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# File 'lib/biointerchange/sofa.rb', line 1227

def self.branch_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000611')
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’. (purl.obolibrary.org/obo/SO_0000593)



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# File 'lib/biointerchange/sofa.rb', line 1197

def self.C_D_box_snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000593')
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. (purl.obolibrary.org/obo/SO_0000581)



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# File 'lib/biointerchange/sofa.rb', line 1173

def self.cap
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000581')
end

.cDNA_match ⇒ `Object`

A match against cDNA sequence. (purl.obolibrary.org/obo/SO_0000689)



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# File 'lib/biointerchange/sofa.rb', line 1383

def self.cDNA_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000689')
end

.CDS ⇒ `Object`

A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. (purl.obolibrary.org/obo/SO_0000316)



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# File 'lib/biointerchange/sofa.rb', line 765

def self.CDS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000316')
end

.CDS_region ⇒ `Object`

A region of a CDS. (purl.obolibrary.org/obo/SO_0000851)



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# File 'lib/biointerchange/sofa.rb', line 1587

def self.CDS_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000851')
end

.centromere ⇒ `Object`

A region of chromosome where the spindle fibers attach during mitosis and meiosis. (purl.obolibrary.org/obo/SO_0000577)



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# File 'lib/biointerchange/sofa.rb', line 1167

def self.centromere
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000577')
end

.chromosomal_structural_element ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000628)



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# File 'lib/biointerchange/sofa.rb', line 1263

def self.chromosomal_structural_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000628')
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. (purl.obolibrary.org/obo/SO_0000340)



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# File 'lib/biointerchange/sofa.rb', line 843

def self.chromosome
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000340')
end

.chromosome_band ⇒ `Object`

A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. (purl.obolibrary.org/obo/SO_0000341)



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# File 'lib/biointerchange/sofa.rb', line 849

def self.chromosome_band
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000341')
end

.chromosome_part ⇒ `Object`

A region of a chromosome. (purl.obolibrary.org/obo/SO_0000830)



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# File 'lib/biointerchange/sofa.rb', line 1527

def self.chromosome_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000830')
end

.cis_splice_site ⇒ `Object`

Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron. (purl.obolibrary.org/obo/SO_0001419)



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# File 'lib/biointerchange/sofa.rb', line 1713

def self.cis_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001419')
end

.cleaved_peptide_region ⇒ `Object`

The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation. (purl.obolibrary.org/obo/SO_0100011)



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# File 'lib/biointerchange/sofa.rb', line 1785

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. (purl.obolibrary.org/obo/SO_0000303)



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# File 'lib/biointerchange/sofa.rb', line 729

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. (purl.obolibrary.org/obo/SO_0000151)



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# File 'lib/biointerchange/sofa.rb', line 495

def self.clone
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000151')
end

.clone_insert ⇒ `Object`

The region of sequence that has been inserted and is being propagated by the clone. (purl.obolibrary.org/obo/SO_0000753)



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# File 'lib/biointerchange/sofa.rb', line 1509

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. (purl.obolibrary.org/obo/SO_0000103)



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# File 'lib/biointerchange/sofa.rb', line 399

def self.clone_insert_end
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000103')
end

.clone_insert_start ⇒ `Object`

The start of the clone insert. (purl.obolibrary.org/obo/SO_0000179)



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# File 'lib/biointerchange/sofa.rb', line 555

def self.clone_insert_start
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000179')
end

.coding_conserved_region ⇒ `Object`

Coding region of sequence similarity by descent from a common ancestor. (purl.obolibrary.org/obo/SO_0000332)



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# File 'lib/biointerchange/sofa.rb', line 813

def self.coding_conserved_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000332')
end

.coding_exon ⇒ `Object`

An exon whereby at least one base is part of a codon (here, ‘codon’ is inclusive of the stop_codon). (purl.obolibrary.org/obo/SO_0000195)



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# File 'lib/biointerchange/sofa.rb', line 597

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. (purl.obolibrary.org/obo/SO_0001215)



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# File 'lib/biointerchange/sofa.rb', line 1665

def self.coding_region_of_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001215')
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. (purl.obolibrary.org/obo/SO_0000360)



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# File 'lib/biointerchange/sofa.rb', line 891

def self.codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000360')
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. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#complete_evidence_for_feature)



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# File 'lib/biointerchange/sofa.rb', line 29

def self.complete_evidence_for_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#complete_evidence_for_feature')
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) (purl.obolibrary.org/obo/SO_1000005)



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# File 'lib/biointerchange/sofa.rb', line 1797

def self.complex_substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000005')
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. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#connects_on)



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# File 'lib/biointerchange/sofa.rb', line 35

def self.connects_on
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#connects_on')
end

.conserved_region ⇒ `Object`

Region of sequence similarity by descent from a common ancestor. (purl.obolibrary.org/obo/SO_0000330)



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# File 'lib/biointerchange/sofa.rb', line 801

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. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#contained_by)



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# File 'lib/biointerchange/sofa.rb', line 41

def self.contained_by
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#contained_by')
end

.contains ⇒ `Object`

The inverse of contained_by. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#contains)



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# File 'lib/biointerchange/sofa.rb', line 47

def self.contains
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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. (purl.obolibrary.org/obo/SO_0000149)



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# File 'lib/biointerchange/sofa.rb', line 483

def self.contig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000149')
end

.copy_number_variation ⇒ `Object`

A variation that increases or decreases the copy number of a given region. (purl.obolibrary.org/obo/SO_0001019)



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# File 'lib/biointerchange/sofa.rb', line 1617

def self.copy_number_variation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001019')
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. (purl.obolibrary.org/obo/SO_0000307)



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# File 'lib/biointerchange/sofa.rb', line 747

def self.CpG_island
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000307')
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. (purl.obolibrary.org/obo/SO_0000727)



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# File 'lib/biointerchange/sofa.rb', line 1491

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. (purl.obolibrary.org/obo/SO_0000177)



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# File 'lib/biointerchange/sofa.rb', line 543

def self.cross_genome_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000177')
end

.databank_entry ⇒ `Object`

The sequence referred to by an entry in a databank such as Genbank or SwissProt. (purl.obolibrary.org/obo/SO_2000061)



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# File 'lib/biointerchange/sofa.rb', line 1821

def self.databank_entry
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_2000061')
end

.decayed_exon ⇒ `Object`

A non-functional descendant of an exon. (purl.obolibrary.org/obo/SO_0000464)



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# File 'lib/biointerchange/sofa.rb', line 1101

def self.decayed_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000464')
end

.deletion ⇒ `Object`

The point at which one or more contiguous nucleotides were excised. (purl.obolibrary.org/obo/SO_0000159)



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# File 'lib/biointerchange/sofa.rb', line 501

def self.deletion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000159')
end

.deletion_junction ⇒ `Object`

The space between two bases in a sequence which marks the position where a deletion has occurred. (purl.obolibrary.org/obo/SO_0000687)



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# File 'lib/biointerchange/sofa.rb', line 1371

def self.deletion_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000687')
end

.derives_from ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#derives_from)



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# File 'lib/biointerchange/sofa.rb', line 53

def self.derives_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#derives_from')
end

.direct_repeat ⇒ `Object`

A repeat where the same sequence is repeated in the same direction. Example: GCTGA—–GCTGA. (purl.obolibrary.org/obo/SO_0000314)



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# File 'lib/biointerchange/sofa.rb', line 753

def self.direct_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000314')
end

.disconnected_from ⇒ `Object`

X is disconnected_from Y iff it is not the case that X overlaps Y. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#disconnected_from)



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# File 'lib/biointerchange/sofa.rb', line 59

def self.disconnected_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#disconnected_from')
end

.dispersed_repeat ⇒ `Object`

A repeat that is located at dispersed sites in the genome. (purl.obolibrary.org/obo/SO_0000658)



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# File 'lib/biointerchange/sofa.rb', line 1335

def self.dispersed_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000658')
end

.ds_oligo ⇒ `Object`

A double stranded oligonucleotide. (purl.obolibrary.org/obo/SO_0000442)



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# File 'lib/biointerchange/sofa.rb', line 1083

def self.ds_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000442')
end

.edited_from ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_from)



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# File 'lib/biointerchange/sofa.rb', line 65

def self.edited_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_from')
end

.edited_to ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_to)



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# File 'lib/biointerchange/sofa.rb', line 71

def self.edited_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_to')
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. (purl.obolibrary.org/obo/SO_0000165)



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# File 'lib/biointerchange/sofa.rb', line 531

def self.enhancer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000165')
end

.enzymatic_RNA ⇒ `Object`

An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein. (purl.obolibrary.org/obo/SO_0000372)



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# File 'lib/biointerchange/sofa.rb', line 915

def self.enzymatic_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000372')
end

.epigenetically_modified_region ⇒ `Object`

A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence. (purl.obolibrary.org/obo/SO_0001720)



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# File 'lib/biointerchange/sofa.rb', line 1761

def self.epigenetically_modified_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001720')
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. (purl.obolibrary.org/obo/SO_0000345)



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# File 'lib/biointerchange/sofa.rb', line 867

def self.EST
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000345')
end

.EST_match ⇒ `Object`

A match against an EST sequence. (purl.obolibrary.org/obo/SO_0000668)



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# File 'lib/biointerchange/sofa.rb', line 1353

def self.EST_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000668')
end

.evidence_for_feature ⇒ `Object`

B is evidence_for_feature A, if an instance of B supports the existence of A. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#evidence_for_feature)



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# File 'lib/biointerchange/sofa.rb', line 77

def self.evidence_for_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#evidence_for_feature')
end

.exemplar_of ⇒ `Object`

X is exemplar of Y if X is the best evidence for Y. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#exemplar_of)



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# File 'lib/biointerchange/sofa.rb', line 83

def self.exemplar_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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. (purl.obolibrary.org/obo/SO_0000147)



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# File 'lib/biointerchange/sofa.rb', line 471

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. (purl.obolibrary.org/obo/SO_0000333)



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# File 'lib/biointerchange/sofa.rb', line 819

def self.exon_junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000333')
end

.exon_region ⇒ `Object`

A region of an exon. (purl.obolibrary.org/obo/SO_0000852)



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# File 'lib/biointerchange/sofa.rb', line 1593

def self.exon_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000852')
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. (purl.obolibrary.org/obo/SO_0001410)



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# File 'lib/biointerchange/sofa.rb', line 1695

def self.experimental_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001410')
end

.experimental_result_region ⇒ `Object`

A region of sequence implicated in an experimental result. (purl.obolibrary.org/obo/SO_0000703)



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# File 'lib/biointerchange/sofa.rb', line 1431

def self.experimental_result_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000703')
end

.expressed_sequence_match ⇒ `Object`

A match to an EST or cDNA sequence. (purl.obolibrary.org/obo/SO_0000102)



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# File 'lib/biointerchange/sofa.rb', line 393

def self.expressed_sequence_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000102')
end

.finished_by ⇒ `Object`

Xy is finished_by Y if Y part of X, and X and Y share a 3’ boundary. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#finished_by)



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# File 'lib/biointerchange/sofa.rb', line 89

def self.finished_by
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#finished_by')
end

.finishes ⇒ `Object`

X finishes Y if X is part_of Y and X and Y share a 3’ or C terminal boundary. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#finishes)



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# File 'lib/biointerchange/sofa.rb', line 95

def self.finishes
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#finishes')
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. (purl.obolibrary.org/obo/SO_0000163)



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# File 'lib/biointerchange/sofa.rb', line 519

def self.five_prime_cis_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000163')
end

.five_prime_coding_exon ⇒ `Object`

The 5’ most coding exon. (purl.obolibrary.org/obo/SO_0000200)



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# File 'lib/biointerchange/sofa.rb', line 621

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. (purl.obolibrary.org/obo/SO_0000196)



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# File 'lib/biointerchange/sofa.rb', line 603

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. (purl.obolibrary.org/obo/SO_0000486)



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# File 'lib/biointerchange/sofa.rb', line 1137

def self.five_prime_coding_exon_noncoding_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000486')
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. (purl.obolibrary.org/obo/SO_0000204)



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# File 'lib/biointerchange/sofa.rb', line 633

def self.five_prime_UTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000204')
end

.flanking_region ⇒ `Object`

The sequences extending on either side of a specific region. (purl.obolibrary.org/obo/SO_0000239)



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# File 'lib/biointerchange/sofa.rb', line 675

def self.flanking_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000239')
end

.gained ⇒ `Object`

X gained Y if X is a variant_of X’ and Y part of X but not X’. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#gained)



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# File 'lib/biointerchange/sofa.rb', line 101

def self.gained
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#gained')
end

.gap ⇒ `Object`

A gap in the sequence of known length. The unknown bases are filled in with N’s. (purl.obolibrary.org/obo/SO_0000730)



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# File 'lib/biointerchange/sofa.rb', line 1497

def self.gap
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000730')
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. (purl.obolibrary.org/obo/SO_0000704)



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# File 'lib/biointerchange/sofa.rb', line 1437

def self.gene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000704')
end

.gene_component_region ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000842)



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# File 'lib/biointerchange/sofa.rb', line 1581

def self.gene_component_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000842')
end

.gene_group ⇒ `Object`

A collection of related genes. (purl.obolibrary.org/obo/SO_0005855)



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# File 'lib/biointerchange/sofa.rb', line 1779

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. – (purl.obolibrary.org/obo/SO_0000752)



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# File 'lib/biointerchange/sofa.rb', line 1503

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. (purl.obolibrary.org/obo/SO_0000831)



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# File 'lib/biointerchange/sofa.rb', line 1533

def self.gene_member_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000831')
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. (purl.obolibrary.org/obo/SO_0000050)



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# File 'lib/biointerchange/sofa.rb', line 369

def self.gene_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000050')
end

.genome_of ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#genome_of)



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# File 'lib/biointerchange/sofa.rb', line 107

def self.genome_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#genome_of')
end

.golden_path ⇒ `Object`

A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence. (purl.obolibrary.org/obo/SO_0000688)



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# File 'lib/biointerchange/sofa.rb', line 1377

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. (purl.obolibrary.org/obo/SO_0000468)



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# File 'lib/biointerchange/sofa.rb', line 1107

def self.golden_path_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000468')
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. (purl.obolibrary.org/obo/SO_0000587)



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# File 'lib/biointerchange/sofa.rb', line 1179

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. (purl.obolibrary.org/obo/SO_0000603)



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# File 'lib/biointerchange/sofa.rb', line 1209

def self.group_II_intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000603')
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. (purl.obolibrary.org/obo/SO_0000602)



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# File 'lib/biointerchange/sofa.rb', line 1203

def self.guide_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000602')
end

.guided_by ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#guided_by)



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# File 'lib/biointerchange/sofa.rb', line 113

def self.guided_by
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#guided_by')
end

.guides ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#guides)



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# File 'lib/biointerchange/sofa.rb', line 119

def self.guides
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#guides')
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. (purl.obolibrary.org/obo/SO_0000380)



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# File 'lib/biointerchange/sofa.rb', line 933

def self.hammerhead_ribozyme
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000380')
end

.has_integral_part ⇒ `Object`

X has_integral_part Y if and only if: X has_part Y and Y part_of X. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_integral_part)



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# File 'lib/biointerchange/sofa.rb', line 125

def self.has_integral_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_integral_part')
end

.has_origin ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_origin)



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# File 'lib/biointerchange/sofa.rb', line 131

def self.has_origin
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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/sofa.rb', line 2777

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. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_part)



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# File 'lib/biointerchange/sofa.rb', line 137

def self.has_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_part')
end

.has_quality ⇒ `Object`

The relationship between a feature and an attribute. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_quality)



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# File 'lib/biointerchange/sofa.rb', line 143

def self.has_quality
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_quality')
end

.homologous_to ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#homologous_to)



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# File 'lib/biointerchange/sofa.rb', line 149

def self.homologous_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#homologous_to')
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. (purl.obolibrary.org/obo/SO_0001063)



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# File 'lib/biointerchange/sofa.rb', line 1653

def self.immature_peptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001063')
end

.insertion ⇒ `Object`

The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. (purl.obolibrary.org/obo/SO_0000667)



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# File 'lib/biointerchange/sofa.rb', line 1347

def self.insertion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000667')
end

.insertion_site ⇒ `Object`

The junction where an insertion occurred. (purl.obolibrary.org/obo/SO_0000366)



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# File 'lib/biointerchange/sofa.rb', line 897

def self.insertion_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000366')
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. (purl.obolibrary.org/obo/SO_0000627)



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# File 'lib/biointerchange/sofa.rb', line 1257

def self.insulator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000627')
end

.integral_part_of ⇒ `Object`

X integral_part_of Y if and only if: X part_of Y and Y has_part X. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#integral_part_of)



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# File 'lib/biointerchange/sofa.rb', line 155

def self.integral_part_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#integral_part_of')
end

.integrated_mobile_genetic_element ⇒ `Object`

An MGE that is integrated into the host chromosome. (purl.obolibrary.org/obo/SO_0001039)



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# File 'lib/biointerchange/sofa.rb', line 1629

def self.integrated_mobile_genetic_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001039')
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. (purl.obolibrary.org/obo/SO_0000605)



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# File 'lib/biointerchange/sofa.rb', line 1215

def self.intergenic_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000605')
end

.interior_coding_exon ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000004)



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# File 'lib/biointerchange/sofa.rb', line 327

def self.interior_coding_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000004')
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. (purl.obolibrary.org/obo/SO_0000188)



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# File 'lib/biointerchange/sofa.rb', line 585

def self.intron
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000188')
end

.inversion ⇒ `Object`

A continuous nucleotide sequence is inverted in the same position. (purl.obolibrary.org/obo/SO_1000036)



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# File 'lib/biointerchange/sofa.rb', line 1809

def self.inversion
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000036')
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. (purl.obolibrary.org/obo/SO_0000294)



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# File 'lib/biointerchange/sofa.rb', line 717

def self.inverted_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000294')
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/sofa.rb', line 1995

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_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_0000013') 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
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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    return true
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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_0000834') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000835') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000836') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000837') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000839') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000841') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000842') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000851') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000852') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001000') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001001') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001002') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001019') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001037') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001039') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001055') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001056') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001059') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001063') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001214') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001215') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001235') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001236') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001248') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001409') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001410') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001411') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001412') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001419') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001420') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001483') 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_0001647') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001654') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001679') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001683') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001720') 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_0005836') 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_0100011') 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_1000036') 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_2000061') 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). (purl.obolibrary.org/obo/SOFA_2_5_2.obo#is_consecutive_sequence_of)



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# File 'lib/biointerchange/sofa.rb', line 161

def self.is_consecutive_sequence_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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)



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# File 'lib/biointerchange/sofa.rb', line 1988

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/sofa.rb', line 2758

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/sofa.rb', line 1828

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/SOFA_2_5_2.obo#adjacent_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#associated_with') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#complete_evidence_for_feature') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#connects_on') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#contained_by') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#contains') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#derives_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#disconnected_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#evidence_for_feature') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#exemplar_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#finished_by') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#finishes') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#gained') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#genome_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#guided_by') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#guides') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_integral_part') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_origin') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_part') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_quality') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#homologous_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#integral_part_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#is_consecutive_sequence_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#lost') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#maximally_overlaps') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#member_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#non_functional_homolog_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#orthologous_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#overlaps') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#paralogous_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#part_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#partial_evidence_for_feature') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#position_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#processed_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#processed_into') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#sequence_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#similar_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#started_by') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#starts') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#transcribed_from') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#transcribed_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#translates_to') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#translation_of') then
    return true
  end
  if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#variant_of') then
    return true
  end
  return false
end

.junction ⇒ `Object`

A sequence_feature with an extent of zero. (purl.obolibrary.org/obo/SO_0000699)



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# File 'lib/biointerchange/sofa.rb', line 1407

def self.junction
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000699')
end

.kozak_sequence ⇒ `Object`

A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5’ UTR and CDS sequence. (purl.obolibrary.org/obo/SO_0001647)



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# File 'lib/biointerchange/sofa.rb', line 1737

def self.kozak_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001647')
end

.large_subunit_rRNA ⇒ `Object`

Ribosomal RNA transcript that structures the large subunit of the ribosome. (purl.obolibrary.org/obo/SO_0000651)



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# File 'lib/biointerchange/sofa.rb', line 1305

def self.large_subunit_rRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000651')
end

.lost ⇒ `Object`

X lost Y if X is a variant_of X’ and Y part of X’ but not X. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#lost)



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# File 'lib/biointerchange/sofa.rb', line 167

def self.lost
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#lost')
end

.match ⇒ `Object`

A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. (purl.obolibrary.org/obo/SO_0000343)



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# File 'lib/biointerchange/sofa.rb', line 855

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. (purl.obolibrary.org/obo/SO_0000039)



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# File 'lib/biointerchange/sofa.rb', line 363

def self.match_part
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000039')
end

.match_set ⇒ `Object`

A collection of match parts. (purl.obolibrary.org/obo/SO_0000038)



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# File 'lib/biointerchange/sofa.rb', line 357

def self.match_set
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000038')
end

.mature_protein_region ⇒ `Object`

The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide. (purl.obolibrary.org/obo/SO_0000419)



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# File 'lib/biointerchange/sofa.rb', line 1065

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. (purl.obolibrary.org/obo/SO_0000233)



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# File 'lib/biointerchange/sofa.rb', line 651

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. (purl.obolibrary.org/obo/SO_0000834)



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# File 'lib/biointerchange/sofa.rb', line 1545

def self.mature_transcript_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000834')
end

.maximally_overlaps ⇒ `Object`

A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#maximally_overlaps)



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# File 'lib/biointerchange/sofa.rb', line 173

def self.maximally_overlaps
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#maximally_overlaps')
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. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#member_of)



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# File 'lib/biointerchange/sofa.rb', line 179

def self.member_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#member_of')
end

.methylated_adenine ⇒ `Object`

A modified base in which adenine has been methylated. (purl.obolibrary.org/obo/SO_0000161)



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# File 'lib/biointerchange/sofa.rb', line 507

def self.methylated_adenine
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000161')
end

.methylated_cytosine ⇒ `Object`

A methylated deoxy-cytosine. (purl.obolibrary.org/obo/SO_0000114)



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# File 'lib/biointerchange/sofa.rb', line 435

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. (purl.obolibrary.org/obo/SO_0000306)



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# File 'lib/biointerchange/sofa.rb', line 741

def self.methylated_DNA_base_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000306')
end

.microsatellite ⇒ `Object`

A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem. (purl.obolibrary.org/obo/SO_0000289)



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# File 'lib/biointerchange/sofa.rb', line 711

def self.microsatellite
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000289')
end

.minisatellite ⇒ `Object`

A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp. (purl.obolibrary.org/obo/SO_0000643)



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# File 'lib/biointerchange/sofa.rb', line 1269

def self.minisatellite
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000643')
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. (purl.obolibrary.org/obo/SO_0000276)



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# File 'lib/biointerchange/sofa.rb', line 705

def self.miRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000276')
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. (purl.obolibrary.org/obo/SO_0001037)



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# File 'lib/biointerchange/sofa.rb', line 1623

def self.mobile_genetic_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001037')
end

.modified_DNA_base ⇒ `Object`

A modified nucleotide, i.e. a nucleotide other than A, T, C. G. (purl.obolibrary.org/obo/SO_0000305)



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# File 'lib/biointerchange/sofa.rb', line 735

def self.modified_DNA_base
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000305')
end

.mRNA ⇒ `Object`

Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. (purl.obolibrary.org/obo/SO_0000234)



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# File 'lib/biointerchange/sofa.rb', line 657

def self.mRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000234')
end

.mRNA_region ⇒ `Object`

A region of an mRNA. (purl.obolibrary.org/obo/SO_0000836)



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# File 'lib/biointerchange/sofa.rb', line 1557

def self.mRNA_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000836')
end

.nc_conserved_region ⇒ `Object`

Non-coding region of sequence similarity by descent from a common ancestor. (purl.obolibrary.org/obo/SO_0000334)



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# File 'lib/biointerchange/sofa.rb', line 825

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. (purl.obolibrary.org/obo/SO_0000483)



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# File 'lib/biointerchange/sofa.rb', line 1125

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. (purl.obolibrary.org/obo/SO_0000655)



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# File 'lib/biointerchange/sofa.rb', line 1323

def self.ncRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000655')
end

.non_functional_homolog_of ⇒ `Object`

A relationship between a pseudogenic feature and its functional ancestor. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#non_functional_homolog_of)



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# File 'lib/biointerchange/sofa.rb', line 185

def self.non_functional_homolog_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#non_functional_homolog_of')
end

.non_transcribed_region ⇒ `Object`

A region of the gene which is not transcribed. (purl.obolibrary.org/obo/SO_0000183)



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# File 'lib/biointerchange/sofa.rb', line 567

def self.non_transcribed_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000183')
end

.noncoding_exon ⇒ `Object`

An exon that does not contain any codons. (purl.obolibrary.org/obo/SO_0000198)



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# File 'lib/biointerchange/sofa.rb', line 615

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. (purl.obolibrary.org/obo/SO_0001214)



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# File 'lib/biointerchange/sofa.rb', line 1659

def self.noncoding_region_of_exon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001214')
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. (purl.obolibrary.org/obo/SO_0000059)



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# File 'lib/biointerchange/sofa.rb', line 381

def self.nuclease_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000059')
end

.nuclease_sensitive_site ⇒ `Object`

A region of nucleotide sequence targeted by a nuclease enzyme. (purl.obolibrary.org/obo/SO_0000684)



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# File 'lib/biointerchange/sofa.rb', line 1365

def self.nuclease_sensitive_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000684')
end

.nucleotide_match ⇒ `Object`

A match against a nucleotide sequence. (purl.obolibrary.org/obo/SO_0000347)



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# File 'lib/biointerchange/sofa.rb', line 873

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. (purl.obolibrary.org/obo/SO_0000714)



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# File 'lib/biointerchange/sofa.rb', line 1455

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. (purl.obolibrary.org/obo/SO_0001654)



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# File 'lib/biointerchange/sofa.rb', line 1743

def self.nucleotide_to_protein_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001654')
end

.oligo ⇒ `Object`

A short oligonucleotide sequence, of length on the order of 10’s of bases; either single or double stranded. (purl.obolibrary.org/obo/SO_0000696)



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# File 'lib/biointerchange/sofa.rb', line 1401

def self.oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000696')
end

.operator ⇒ `Object`

A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon. (purl.obolibrary.org/obo/SO_0000057)



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# File 'lib/biointerchange/sofa.rb', line 375

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. (purl.obolibrary.org/obo/SO_0000178)



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# File 'lib/biointerchange/sofa.rb', line 549

def self.operon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000178')
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. (purl.obolibrary.org/obo/SO_0000236)



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# File 'lib/biointerchange/sofa.rb', line 669

def self.ORF
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000236')
end

.origin_of_replication ⇒ `Object`

The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies. (purl.obolibrary.org/obo/SO_0000296)



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# File 'lib/biointerchange/sofa.rb', line 723

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. (purl.obolibrary.org/obo/SO_0000724)



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# File 'lib/biointerchange/sofa.rb', line 1479

def self.oriT
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000724')
end

.orthologous_to ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#orthologous_to)



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# File 'lib/biointerchange/sofa.rb', line 191

def self.orthologous_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#orthologous_to')
end

.overlaps ⇒ `Object`

X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#overlaps)



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# File 'lib/biointerchange/sofa.rb', line 197

def self.overlaps
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#overlaps')
end

.paired_end_fragment ⇒ `Object`

An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair). (purl.obolibrary.org/obo/SO_0001790)



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# File 'lib/biointerchange/sofa.rb', line 1767

def self.paired_end_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001790')
end

.paralogous_to ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#paralogous_to)



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# File 'lib/biointerchange/sofa.rb', line 203

def self.paralogous_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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/SOFA_2_5_2.obo#part_of)



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# File 'lib/biointerchange/sofa.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/SOFA_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. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#partial_evidence_for_feature)



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# File 'lib/biointerchange/sofa.rb', line 209

def self.partial_evidence_for_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#partial_evidence_for_feature')
end

.PCR_product ⇒ `Object`

A region amplified by a PCR reaction. (purl.obolibrary.org/obo/SO_0000006)



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# File 'lib/biointerchange/sofa.rb', line 339

def self.PCR_product
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000006')
end

.peptide_localization_signal ⇒ `Object`

A region of peptide sequence used to target the polypeptide molecule to a specific organelle. (purl.obolibrary.org/obo/SO_0001527)



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# File 'lib/biointerchange/sofa.rb', line 1731

def self.peptide_localization_signal
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001527')
end

.point_mutation ⇒ `Object`

A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. (purl.obolibrary.org/obo/SO_1000008)



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# File 'lib/biointerchange/sofa.rb', line 1803

def self.point_mutation
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000008')
end

.polyA_sequence ⇒ `Object`

Sequence of about 100 nucleotides of A added to the 3’ end of most eukaryotic mRNAs. (purl.obolibrary.org/obo/SO_0000610)



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# File 'lib/biointerchange/sofa.rb', line 1221

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. (purl.obolibrary.org/obo/SO_0000551)



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# File 'lib/biointerchange/sofa.rb', line 1155

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. (purl.obolibrary.org/obo/SO_0000553)



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# File 'lib/biointerchange/sofa.rb', line 1161

def self.polyA_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000553')
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. (purl.obolibrary.org/obo/SO_0000104)



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# File 'lib/biointerchange/sofa.rb', line 405

def self.polypeptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000104')
end

.polypeptide_region ⇒ `Object`

Biological sequence region that can be assigned to a specific subsequence of a polypeptide. (purl.obolibrary.org/obo/SO_0000839)



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# File 'lib/biointerchange/sofa.rb', line 1569

def self.polypeptide_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000839')
end

.polypyrimidine_tract ⇒ `Object`

The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing. (purl.obolibrary.org/obo/SO_0000612)



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# File 'lib/biointerchange/sofa.rb', line 1233

def self.polypyrimidine_tract
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000612')
end

.position_of ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#position_of)



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# File 'lib/biointerchange/sofa.rb', line 215

def self.position_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#position_of')
end

.possible_assembly_error ⇒ `Object`

A region of sequence where there may have been an error in the assembly. (purl.obolibrary.org/obo/SO_0000702)



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# File 'lib/biointerchange/sofa.rb', line 1425

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. (purl.obolibrary.org/obo/SO_0000701)



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# File 'lib/biointerchange/sofa.rb', line 1419

def self.possible_base_call_error
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000701')
end

.primary_transcript ⇒ `Object`

A transcript that in its initial state requires modification to be functional. (purl.obolibrary.org/obo/SO_0000185)



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# File 'lib/biointerchange/sofa.rb', line 573

def self.primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000185')
end

.primary_transcript_region ⇒ `Object`

A part of a primary transcript. (purl.obolibrary.org/obo/SO_0000835)



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# File 'lib/biointerchange/sofa.rb', line 1551

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. (purl.obolibrary.org/obo/SO_0000112)



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# File 'lib/biointerchange/sofa.rb', line 423

def self.primer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000112')
end

.processed_from ⇒ `Object`

Inverse of processed_into. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#processed_from)



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# File 'lib/biointerchange/sofa.rb', line 221

def self.processed_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#processed_from')
end

.processed_into ⇒ `Object`

X is processed_into Y if a region X is modified to create Y. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#processed_into)



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# File 'lib/biointerchange/sofa.rb', line 227

def self.processed_into
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#processed_into')
end

.promoter ⇒ `Object`

A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. (purl.obolibrary.org/obo/SO_0000167)



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# File 'lib/biointerchange/sofa.rb', line 537

def self.promoter
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000167')
end

.protein_binding_site ⇒ `Object`

A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules. (purl.obolibrary.org/obo/SO_0000410)



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# File 'lib/biointerchange/sofa.rb', line 1041

def self.protein_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000410')
end

.protein_coding_primary_transcript ⇒ `Object`

A primary transcript that, at least in part, encodes one or more proteins. (purl.obolibrary.org/obo/SO_0000120)



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# File 'lib/biointerchange/sofa.rb', line 441

def self.protein_coding_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000120')
end

.protein_match ⇒ `Object`

A match against a protein sequence. (purl.obolibrary.org/obo/SO_0000349)



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# File 'lib/biointerchange/sofa.rb', line 879

def self.protein_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000349')
end

.proviral_region ⇒ `Object`

A viral sequence which has integrated into a host genome. (purl.obolibrary.org/obo/SO_0000113)



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# File 'lib/biointerchange/sofa.rb', line 429

def self.proviral_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000113')
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). (www.ucl.ac.uk/~ucbhjow/b241/glossary.html) (purl.obolibrary.org/obo/SO_0000336)



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# File 'lib/biointerchange/sofa.rb', line 831

def self.pseudogene
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000336')
end

.pseudogenic_region ⇒ `Object`

A non-functional descendent of a functional entity. (purl.obolibrary.org/obo/SO_0000462)



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# File 'lib/biointerchange/sofa.rb', line 1095

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. (purl.obolibrary.org/obo/SO_0000777)



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# File 'lib/biointerchange/sofa.rb', line 1515

def self.pseudogenic_rRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000777')
end

.pseudogenic_tRNA ⇒ `Object`

A non functional descendent of a tRNA. (purl.obolibrary.org/obo/SO_0000778)



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# File 'lib/biointerchange/sofa.rb', line 1521

def self.pseudogenic_tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000778')
end

.rasiRNA ⇒ `Object`

A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements. (purl.obolibrary.org/obo/SO_0000454)



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# File 'lib/biointerchange/sofa.rb', line 1089

def self.rasiRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000454')
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. (purl.obolibrary.org/obo/SO_0000150)



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# File 'lib/biointerchange/sofa.rb', line 489

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. (purl.obolibrary.org/obo/SO_0000007)



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# File 'lib/biointerchange/sofa.rb', line 345

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. (purl.obolibrary.org/obo/SO_0000717)



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# File 'lib/biointerchange/sofa.rb', line 1467

def self.reading_frame
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000717')
end

.reagent ⇒ `Object`

A sequence used in experiment. (purl.obolibrary.org/obo/SO_0000695)



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# File 'lib/biointerchange/sofa.rb', line 1395

def self.reagent
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000695')
end

.recombined_from ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_from)



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# File 'lib/biointerchange/sofa.rb', line 233

def self.recombined_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_from')
end

.recombined_to ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_to)



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# File 'lib/biointerchange/sofa.rb', line 239

def self.recombined_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_to')
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. (purl.obolibrary.org/obo/SO_0000001)



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# File 'lib/biointerchange/sofa.rb', line 321

def self.region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000001')
end

.regulatory_region ⇒ `Object`

A region of sequence that is involved in the control of a biological process. (purl.obolibrary.org/obo/SO_0005836)



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# File 'lib/biointerchange/sofa.rb', line 1773

def self.regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005836')
end

.regulon ⇒ `Object`

A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal. (purl.obolibrary.org/obo/SO_1001284)



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# File 'lib/biointerchange/sofa.rb', line 1815

def self.regulon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001284')
end

.remark ⇒ `Object`

A comment about the sequence. (purl.obolibrary.org/obo/SO_0000700)



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# File 'lib/biointerchange/sofa.rb', line 1413

def self.remark
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000700')
end

.repeat_family ⇒ `Object`

A group of characterized repeat sequences. (purl.obolibrary.org/obo/SO_0000187)



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# File 'lib/biointerchange/sofa.rb', line 579

def self.repeat_family
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000187')
end

.repeat_region ⇒ `Object`

A region of sequence containing one or more repeat units. (purl.obolibrary.org/obo/SO_0000657)



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# File 'lib/biointerchange/sofa.rb', line 1329

def self.repeat_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000657')
end

.replicon ⇒ `Object`

A region containing at least one unique origin of replication and a unique termination site. (purl.obolibrary.org/obo/SO_0001235)



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# File 'lib/biointerchange/sofa.rb', line 1671

def self.replicon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001235')
end

.restriction_fragment ⇒ `Object`

A region of polynucleotide sequence produced by digestion with a restriction endonuclease. (purl.obolibrary.org/obo/SO_0000412)



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# File 'lib/biointerchange/sofa.rb', line 1047

def self.restriction_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000412')
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. (purl.obolibrary.org/obo/SO_0000193)



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# File 'lib/biointerchange/sofa.rb', line 591

def self.RFLP_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000193')
end

.ribosome_entry_site ⇒ `Object`

Region in mRNA where ribosome assembles. (purl.obolibrary.org/obo/SO_0000139)



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# File 'lib/biointerchange/sofa.rb', line 447

def self.ribosome_entry_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000139')
end

.ribozyme ⇒ `Object`

An RNA with catalytic activity. (purl.obolibrary.org/obo/SO_0000374)



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# File 'lib/biointerchange/sofa.rb', line 921

def self.ribozyme
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000374')
end

.RNA_motif ⇒ `Object`

A motif that is active in RNA sequence. (purl.obolibrary.org/obo/SO_0000715)



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# File 'lib/biointerchange/sofa.rb', line 1461

def self.RNA_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000715')
end

.RNAi_reagent ⇒ `Object`

A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference. (purl.obolibrary.org/obo/SO_0000337)



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# File 'lib/biointerchange/sofa.rb', line 837

def self.RNAi_reagent
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000337')
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. (purl.obolibrary.org/obo/SO_0000385)



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# File 'lib/biointerchange/sofa.rb', line 939

def self.RNase_MRP_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000385')
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. (purl.obolibrary.org/obo/SO_0000386)



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# File 'lib/biointerchange/sofa.rb', line 945

def self.RNase_P_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000386')
end

.rRNA ⇒ `Object`

RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity. (purl.obolibrary.org/obo/SO_0000252)



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# File 'lib/biointerchange/sofa.rb', line 681

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. (purl.obolibrary.org/obo/SO_0001000)



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# File 'lib/biointerchange/sofa.rb', line 1599

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. (purl.obolibrary.org/obo/SO_0000407)



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# File 'lib/biointerchange/sofa.rb', line 1029

def self.rRNA_18S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000407')
end

.rRNA_23S ⇒ `Object`

A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome. (purl.obolibrary.org/obo/SO_0001001)



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# File 'lib/biointerchange/sofa.rb', line 1605

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. (purl.obolibrary.org/obo/SO_0001002)



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# File 'lib/biointerchange/sofa.rb', line 1611

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. (purl.obolibrary.org/obo/SO_0000653)



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# File 'lib/biointerchange/sofa.rb', line 1317

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. (purl.obolibrary.org/obo/SO_0000375)



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# File 'lib/biointerchange/sofa.rb', line 927

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. (purl.obolibrary.org/obo/SO_0000652)



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# File 'lib/biointerchange/sofa.rb', line 1311

def self.rRNA_5S
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000652')
end

.rRNA_large_subunit_primary_transcript ⇒ `Object`

A primary transcript encoding a large ribosomal subunit RNA. (purl.obolibrary.org/obo/SO_0000325)



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# File 'lib/biointerchange/sofa.rb', line 789

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. (purl.obolibrary.org/obo/SO_0000209)



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# File 'lib/biointerchange/sofa.rb', line 645

def self.rRNA_primary_transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000209')
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. (purl.obolibrary.org/obo/SO_0000326)



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# File 'lib/biointerchange/sofa.rb', line 795

def self.SAGE_tag
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000326')
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. (purl.obolibrary.org/obo/SO_0000005)



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# File 'lib/biointerchange/sofa.rb', line 333

def self.satellite_DNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000005')
end

.scRNA ⇒ `Object`

A small non coding RNA sequence, present in the cytoplasm. (purl.obolibrary.org/obo/SO_0000013)



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# File 'lib/biointerchange/sofa.rb', line 351

def self.scRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000013')
end

.sequence_alteration ⇒ `Object`

A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. (purl.obolibrary.org/obo/SO_0001059)



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# File 'lib/biointerchange/sofa.rb', line 1647

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. (purl.obolibrary.org/obo/SO_0000353)



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# File 'lib/biointerchange/sofa.rb', line 885

def self.sequence_assembly
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000353')
end

.sequence_difference ⇒ `Object`

A region where the sequence differs from that of a specified sequence. (purl.obolibrary.org/obo/SO_0000413)



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# File 'lib/biointerchange/sofa.rb', line 1053

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. (purl.obolibrary.org/obo/SO_0000110)



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# File 'lib/biointerchange/sofa.rb', line 417

def self.sequence_feature
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000110')
end

.sequence_motif ⇒ `Object`

A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance. (purl.obolibrary.org/obo/SO_0001683)



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# File 'lib/biointerchange/sofa.rb', line 1755

def self.sequence_motif
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001683')
end

.sequence_of ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#sequence_of)



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# File 'lib/biointerchange/sofa.rb', line 245

def self.sequence_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#sequence_of')
end

.Sequence_Ontology ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SO_0000000)



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# File 'lib/biointerchange/sofa.rb', line 315

def self.Sequence_Ontology
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000000')
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. (purl.obolibrary.org/obo/SO_0000109)



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# File 'lib/biointerchange/sofa.rb', line 411

def self.sequence_variant_obs
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000109')
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. (purl.obolibrary.org/obo/SO_0000418)



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# File 'lib/biointerchange/sofa.rb', line 1059

def self.signal_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000418')
end

.silencer ⇒ `Object`

A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control. (purl.obolibrary.org/obo/SO_0000625)



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# File 'lib/biointerchange/sofa.rb', line 1251

def self.silencer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000625')
end

.similar_to ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#similar_to)



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# File 'lib/biointerchange/sofa.rb', line 251

def self.similar_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#similar_to')
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. (purl.obolibrary.org/obo/SO_0000646)



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# File 'lib/biointerchange/sofa.rb', line 1287

def self.siRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000646')
end

.small_regulatory_ncRNA ⇒ `Object`

A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression. (purl.obolibrary.org/obo/SO_0000370)



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# File 'lib/biointerchange/sofa.rb', line 909

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. (purl.obolibrary.org/obo/SO_0000650)



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# File 'lib/biointerchange/sofa.rb', line 1299

def self.small_subunit_rRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000650')
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. (purl.obolibrary.org/obo/SO_0000275)



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# File 'lib/biointerchange/sofa.rb', line 699

def self.snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000275')
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. (purl.obolibrary.org/obo/SO_0000694)



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# File 'lib/biointerchange/sofa.rb', line 1389

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. (purl.obolibrary.org/obo/SO_0000274)



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# File 'lib/biointerchange/sofa.rb', line 693

def self.snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000274')
end

.SNV ⇒ `Object`

SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist. (purl.obolibrary.org/obo/SO_0001483)



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# File 'lib/biointerchange/sofa.rb', line 1725

def self.SNV
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001483')
end

.splice_enhancer ⇒ `Object`

Region of a transcript that regulates splicing. (purl.obolibrary.org/obo/SO_0000344)



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# File 'lib/biointerchange/sofa.rb', line 861

def self.splice_enhancer
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000344')
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. (purl.obolibrary.org/obo/SO_0000162)



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# File 'lib/biointerchange/sofa.rb', line 513

def self.splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000162')
end

.spliceosomal_intron ⇒ `Object`

An intron which is spliced by the spliceosome. (purl.obolibrary.org/obo/SO_0000662)



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# File 'lib/biointerchange/sofa.rb', line 1341

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. (purl.obolibrary.org/obo/SO_0000841)



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# File 'lib/biointerchange/sofa.rb', line 1575

def self.spliceosomal_intron_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000841')
end

.splicing_regulatory_region ⇒ `Object`

A regulatory_region that modulates splicing. (purl.obolibrary.org/obo/SO_0001056)



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# File 'lib/biointerchange/sofa.rb', line 1641

def self.splicing_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001056')
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. (purl.obolibrary.org/obo/SO_0000590)



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# File 'lib/biointerchange/sofa.rb', line 1191

def self.SRP_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000590')
end

.ss_oligo ⇒ `Object`

A single stranded oligonucleotide. (purl.obolibrary.org/obo/SO_0000441)



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# File 'lib/biointerchange/sofa.rb', line 1077

def self.ss_oligo
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000441')
end

.start_codon ⇒ `Object`

First codon to be translated by a ribosome. (purl.obolibrary.org/obo/SO_0000318)



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# File 'lib/biointerchange/sofa.rb', line 771

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. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#started_by)



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# File 'lib/biointerchange/sofa.rb', line 257

def self.started_by
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#starts)



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# File 'lib/biointerchange/sofa.rb', line 263

def self.starts
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#starts')
end

.stop_codon ⇒ `Object`

In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis. (purl.obolibrary.org/obo/SO_0000319)



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# File 'lib/biointerchange/sofa.rb', line 777

def self.stop_codon
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000319')
end

.stRNA ⇒ `Object`

Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans. (purl.obolibrary.org/obo/SO_0000649)



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# File 'lib/biointerchange/sofa.rb', line 1293

def self.stRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000649')
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. (purl.obolibrary.org/obo/SO_0000331)



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# File 'lib/biointerchange/sofa.rb', line 807

def self.STS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000331')
end

.substitution ⇒ `Object`

A sequence alteration where the length of the change in the variant is the same as that of the reference. (purl.obolibrary.org/obo/SO_1000002)



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# File 'lib/biointerchange/sofa.rb', line 1791

def self.substitution
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000002')
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. (purl.obolibrary.org/obo/SO_0000148)



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# File 'lib/biointerchange/sofa.rb', line 477

def self.supercontig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000148')
end

.tag ⇒ `Object`

A nucleotide sequence that may be used to identify a larger sequence. (purl.obolibrary.org/obo/SO_0000324)



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# File 'lib/biointerchange/sofa.rb', line 783

def self.tag
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000324')
end

.tandem_repeat ⇒ `Object`

Two or more adjcent copies of a region (of length greater than 1). (purl.obolibrary.org/obo/SO_0000705)



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# File 'lib/biointerchange/sofa.rb', line 1443

def self.tandem_repeat
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000705')
end

.telomerase_RNA ⇒ `Object`

The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA. (purl.obolibrary.org/obo/SO_0000390)



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# File 'lib/biointerchange/sofa.rb', line 951

def self.telomerase_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000390')
end

.telomere ⇒ `Object`

A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end. (purl.obolibrary.org/obo/SO_0000624)



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# File 'lib/biointerchange/sofa.rb', line 1245

def self.telomere
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000624')
end

.terminator ⇒ `Object`

The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. (purl.obolibrary.org/obo/SO_0000141)



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# File 'lib/biointerchange/sofa.rb', line 459

def self.terminator
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000141')
end

.TF_binding_site ⇒ `Object`

A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]. (purl.obolibrary.org/obo/SO_0000235)



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# File 'lib/biointerchange/sofa.rb', line 663

def self.TF_binding_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000235')
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. (purl.obolibrary.org/obo/SO_0000164)



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# File 'lib/biointerchange/sofa.rb', line 525

def self.three_prime_cis_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000164')
end

.three_prime_coding_exon_coding_region ⇒ `Object`

The sequence of the three_prime_coding_exon that codes for protein. (purl.obolibrary.org/obo/SO_0000197)



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# File 'lib/biointerchange/sofa.rb', line 609

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. (purl.obolibrary.org/obo/SO_0000484)



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# File 'lib/biointerchange/sofa.rb', line 1131

def self.three_prime_coding_exon_noncoding_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000484')
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. (purl.obolibrary.org/obo/SO_0000205)



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# File 'lib/biointerchange/sofa.rb', line 639

def self.three_prime_UTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000205')
end

.tiling_path ⇒ `Object`

A set of regions which overlap with minimal polymorphism to form a linear sequence. (purl.obolibrary.org/obo/SO_0000472)



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# File 'lib/biointerchange/sofa.rb', line 1113

def self.tiling_path
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000472')
end

.tiling_path_fragment ⇒ `Object`

A piece of sequence that makes up a tiling_path (SO:0000472). (purl.obolibrary.org/obo/SO_0000474)



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# File 'lib/biointerchange/sofa.rb', line 1119

def self.tiling_path_fragment
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000474')
end

.topologically_defined_region ⇒ `Object`

A region that is defined according to its relations with other regions within the same sequence. (purl.obolibrary.org/obo/SO_0001412)



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# File 'lib/biointerchange/sofa.rb', line 1707

def self.topologically_defined_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001412')
end

.trans_splice_acceptor_site ⇒ `Object`

The 3’ splice site of the acceptor primary transcript. (purl.obolibrary.org/obo/SO_0000706)



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# File 'lib/biointerchange/sofa.rb', line 1449

def self.trans_splice_acceptor_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000706')
end

.trans_splice_site ⇒ `Object`

Primary transcript region bordering trans-splice junction. (purl.obolibrary.org/obo/SO_0001420)



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# File 'lib/biointerchange/sofa.rb', line 1719

def self.trans_splice_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001420')
end

.trans_spliced_from ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_from)



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# File 'lib/biointerchange/sofa.rb', line 269

def self.trans_spliced_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_from')
end

.trans_spliced_to ⇒ `Object`

– No comment or description provided. – (purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_to)



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# File 'lib/biointerchange/sofa.rb', line 275

def self.trans_spliced_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_to')
end

.transcribed_from ⇒ `Object`

X is transcribed_from Y if X is synthesized from template Y. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#transcribed_from)



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# File 'lib/biointerchange/sofa.rb', line 281

def self.transcribed_from
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_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. (purl.obolibrary.org/obo/SO_0000502)



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# File 'lib/biointerchange/sofa.rb', line 1149

def self.transcribed_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000502')
end

.transcribed_to ⇒ `Object`

Inverse of transcribed_from. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#transcribed_to)



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# File 'lib/biointerchange/sofa.rb', line 287

def self.transcribed_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#transcribed_to')
end

.transcript ⇒ `Object`

An RNA synthesized on a DNA or RNA template by an RNA polymerase. (purl.obolibrary.org/obo/SO_0000673)



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# File 'lib/biointerchange/sofa.rb', line 1359

def self.transcript
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000673')
end

.transcript_region ⇒ `Object`

A region of a transcript. (purl.obolibrary.org/obo/SO_0000833)



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# File 'lib/biointerchange/sofa.rb', line 1539

def self.transcript_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000833')
end

.transcription_end_site ⇒ `Object`

The base where transcription ends. (purl.obolibrary.org/obo/SO_0000616)



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# File 'lib/biointerchange/sofa.rb', line 1239

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. (purl.obolibrary.org/obo/SO_0001679)



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# File 'lib/biointerchange/sofa.rb', line 1749

def self.transcription_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001679')
end

.transcriptional_cis_regulatory_region ⇒ `Object`

A regulatory_region that modulates the transcription of a gene or genes. (purl.obolibrary.org/obo/SO_0001055)



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# File 'lib/biointerchange/sofa.rb', line 1635

def self.transcriptional_cis_regulatory_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001055')
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). (purl.obolibrary.org/obo/SO_0000725)



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# File 'lib/biointerchange/sofa.rb', line 1485

def self.transit_peptide
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000725')
end

.translated_nucleotide_match ⇒ `Object`

A match against a translated sequence. (purl.obolibrary.org/obo/SO_0000181)



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# File 'lib/biointerchange/sofa.rb', line 561

def self.translated_nucleotide_match
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000181')
end

.translates_to ⇒ `Object`

Inverse of translation _of. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#translates_to)



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# File 'lib/biointerchange/sofa.rb', line 293

def self.translates_to
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#translates_to')
end

.translation_of ⇒ `Object`

X is translation of Y if Y is translated by ribosome to create X. (purl.obolibrary.org/obo/SOFA_2_5_2.obo#translation_of)



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# File 'lib/biointerchange/sofa.rb', line 299

def self.translation_of
  return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#translation_of')
end

.transposable_element ⇒ `Object`

A transposon or insertion sequence. An element that can insert in a variety of DNA sequences. (purl.obolibrary.org/obo/SO_0000101)



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# File 'lib/biointerchange/sofa.rb', line 387

def self.transposable_element
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000101')
end

.transposable_element_insertion_site ⇒ `Object`

The junction in a genome where a transposable_element has inserted. (purl.obolibrary.org/obo/SO_0000368)



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# File 'lib/biointerchange/sofa.rb', line 903

def self.transposable_element_insertion_site
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000368')
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. (purl.obolibrary.org/obo/SO_0000253)



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# File 'lib/biointerchange/sofa.rb', line 687

def self.tRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000253')
end

.TSS ⇒ `Object`

The first base where RNA polymerase begins to synthesize the RNA transcript. (purl.obolibrary.org/obo/SO_0000315)



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# File 'lib/biointerchange/sofa.rb', line 759

def self.TSS
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000315')
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. (purl.obolibrary.org/obo/SO_0000398)



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# File 'lib/biointerchange/sofa.rb', line 999

def self.U11_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000398')
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. (purl.obolibrary.org/obo/SO_0000399)



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# File 'lib/biointerchange/sofa.rb', line 1005

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. (purl.obolibrary.org/obo/SO_0000403)



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# File 'lib/biointerchange/sofa.rb', line 1011

def self.U14_snoRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000403')
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. (purl.obolibrary.org/obo/SO_0000391)



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# File 'lib/biointerchange/sofa.rb', line 957

def self.U1_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000391')
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. (purl.obolibrary.org/obo/SO_0000392)



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# File 'lib/biointerchange/sofa.rb', line 963

def self.U2_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000392')
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. (purl.obolibrary.org/obo/SO_0000393)



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# File 'lib/biointerchange/sofa.rb', line 969

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). (purl.obolibrary.org/obo/SO_0000394)



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# File 'lib/biointerchange/sofa.rb', line 975

def self.U4atac_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000394')
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. (purl.obolibrary.org/obo/SO_0000395)



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# File 'lib/biointerchange/sofa.rb', line 981

def self.U5_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000395')
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. (purl.obolibrary.org/obo/SO_0000396)



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# File 'lib/biointerchange/sofa.rb', line 987

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). (purl.obolibrary.org/obo/SO_0000397)



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# File 'lib/biointerchange/sofa.rb', line 993

def self.U6atac_snRNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000397')
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. (purl.obolibrary.org/obo/SO_0000719)



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# File 'lib/biointerchange/sofa.rb', line 1473

def self.ultracontig
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000719')
end

.UTR ⇒ `Object`

Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated. (purl.obolibrary.org/obo/SO_0000203)



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# File 'lib/biointerchange/sofa.rb', line 627

def self.UTR
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000203')
end

.UTR_region ⇒ `Object`

A region of UTR. (purl.obolibrary.org/obo/SO_0000837)



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# File 'lib/biointerchange/sofa.rb', line 1563

def self.UTR_region
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000837')
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/SOFA_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)



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# File 'lib/biointerchange/sofa.rb', line 309

def self.variant_of
  return [ RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#variant_of'), RDF::URI.new('http://purl.obolibrary.org/obo/anonymous#variant_of') ]
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. (purl.obolibrary.org/obo/SO_0000404)



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# File 'lib/biointerchange/sofa.rb', line 1017

def self.vault_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000404')
end

.virtual_sequence ⇒ `Object`

A continuous piece of sequence similar to the ‘virtual contig’ concept of the Ensembl database. (purl.obolibrary.org/obo/SO_0000499)



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# File 'lib/biointerchange/sofa.rb', line 1143

def self.virtual_sequence
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000499')
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.



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# File 'lib/biointerchange/sofa.rb', line 2769

def self.with_parent(uris, parent)
  return uris.select { |uri| has_parent?(uri, parent) }
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. (purl.obolibrary.org/obo/SO_0000405)



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# File 'lib/biointerchange/sofa.rb', line 1023

def self.Y_RNA
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000405')
end

Class: BioInterchange::SOFA

Class Method Summary collapse

Class Method Details

.adjacent_to ⇒ Object

.antisense_primary_transcript ⇒ Object

.antisense_RNA ⇒ Object

.ARS ⇒ Object

.assembly ⇒ Object

.assembly_component ⇒ Object

.associated_with ⇒ Object

.attenuator ⇒ Object

.autocatalytically_spliced_intron ⇒ Object

.base ⇒ Object

.binding_site ⇒ Object

.biological_region ⇒ Object

.biomaterial_region ⇒ Object

.branch_site ⇒ Object

.C_D_box_snoRNA ⇒ Object

.cap ⇒ Object

.cDNA_match ⇒ Object

.CDS ⇒ Object

.CDS_region ⇒ Object

.centromere ⇒ Object

.chromosomal_structural_element ⇒ Object

.chromosome ⇒ Object

.chromosome_band ⇒ Object

.chromosome_part ⇒ Object

.cis_splice_site ⇒ Object

.cleaved_peptide_region ⇒ Object

.clip ⇒ Object

.clone ⇒ Object

.clone_insert ⇒ Object

.clone_insert_end ⇒ Object

.clone_insert_start ⇒ Object

.coding_conserved_region ⇒ Object

.coding_exon ⇒ Object

.coding_region_of_exon ⇒ Object

.codon ⇒ Object

.complete_evidence_for_feature ⇒ Object

.complex_substitution ⇒ Object

.connects_on ⇒ Object

.conserved_region ⇒ Object

.contained_by ⇒ Object

.contains ⇒ Object

.contig ⇒ Object

.copy_number_variation ⇒ Object

.CpG_island ⇒ Object

.CRM ⇒ Object

.cross_genome_match ⇒ Object

.databank_entry ⇒ Object

.decayed_exon ⇒ Object

.deletion ⇒ Object

.deletion_junction ⇒ Object

.derives_from ⇒ Object

.direct_repeat ⇒ Object

.disconnected_from ⇒ Object

.dispersed_repeat ⇒ Object

.ds_oligo ⇒ Object

.edited_from ⇒ Object

.edited_to ⇒ Object

.enhancer ⇒ Object

.enzymatic_RNA ⇒ Object

.epigenetically_modified_region ⇒ Object

.EST ⇒ Object

.EST_match ⇒ Object

.evidence_for_feature ⇒ Object

.exemplar_of ⇒ Object

.exon ⇒ Object

.exon_junction ⇒ Object

.exon_region ⇒ Object

.experimental_feature ⇒ Object

.experimental_result_region ⇒ Object

.expressed_sequence_match ⇒ Object

.finished_by ⇒ Object

.finishes ⇒ Object

.five_prime_cis_splice_site ⇒ Object

.five_prime_coding_exon ⇒ Object

.five_prime_coding_exon_coding_region ⇒ Object

.five_prime_coding_exon_noncoding_region ⇒ Object

.five_prime_UTR ⇒ Object

.adjacent_to ⇒ `Object`

.antisense_primary_transcript ⇒ `Object`

.antisense_RNA ⇒ `Object`

.ARS ⇒ `Object`

.assembly ⇒ `Object`

.assembly_component ⇒ `Object`

.associated_with ⇒ `Object`

.attenuator ⇒ `Object`

.autocatalytically_spliced_intron ⇒ `Object`

.base ⇒ `Object`

.binding_site ⇒ `Object`

.biological_region ⇒ `Object`

.biomaterial_region ⇒ `Object`

.branch_site ⇒ `Object`

.C_D_box_snoRNA ⇒ `Object`

.cap ⇒ `Object`

.cDNA_match ⇒ `Object`

.CDS ⇒ `Object`

.CDS_region ⇒ `Object`

.centromere ⇒ `Object`

.chromosomal_structural_element ⇒ `Object`

.chromosome ⇒ `Object`

.chromosome_band ⇒ `Object`

.chromosome_part ⇒ `Object`

.cis_splice_site ⇒ `Object`

.cleaved_peptide_region ⇒ `Object`

.clip ⇒ `Object`

.clone ⇒ `Object`

.clone_insert ⇒ `Object`

.clone_insert_end ⇒ `Object`

.clone_insert_start ⇒ `Object`

.coding_conserved_region ⇒ `Object`

.coding_exon ⇒ `Object`

.coding_region_of_exon ⇒ `Object`

.codon ⇒ `Object`

.complete_evidence_for_feature ⇒ `Object`

.complex_substitution ⇒ `Object`

.connects_on ⇒ `Object`

.conserved_region ⇒ `Object`

.contained_by ⇒ `Object`

.contains ⇒ `Object`

.contig ⇒ `Object`

.copy_number_variation ⇒ `Object`

.CpG_island ⇒ `Object`

.CRM ⇒ `Object`

.cross_genome_match ⇒ `Object`

.databank_entry ⇒ `Object`

.decayed_exon ⇒ `Object`

.deletion ⇒ `Object`

.deletion_junction ⇒ `Object`

.derives_from ⇒ `Object`

.direct_repeat ⇒ `Object`

.disconnected_from ⇒ `Object`

.dispersed_repeat ⇒ `Object`

.ds_oligo ⇒ `Object`

.edited_from ⇒ `Object`

.edited_to ⇒ `Object`

.enhancer ⇒ `Object`

.enzymatic_RNA ⇒ `Object`

.epigenetically_modified_region ⇒ `Object`

.EST ⇒ `Object`

.EST_match ⇒ `Object`

.evidence_for_feature ⇒ `Object`

.exemplar_of ⇒ `Object`

.exon ⇒ `Object`

.exon_junction ⇒ `Object`

.exon_region ⇒ `Object`

.experimental_feature ⇒ `Object`

.experimental_result_region ⇒ `Object`

.expressed_sequence_match ⇒ `Object`

.finished_by ⇒ `Object`

.finishes ⇒ `Object`

.five_prime_cis_splice_site ⇒ `Object`

.five_prime_coding_exon ⇒ `Object`

.five_prime_coding_exon_coding_region ⇒ `Object`

.five_prime_coding_exon_noncoding_region ⇒ `Object`

.five_prime_UTR ⇒ `Object`

.flanking_region ⇒ `Object`

.gained ⇒ `Object`

.gap ⇒ `Object`