Module: BELParser::Resources

Defined in:
lib/bel_parser/resources.rb

Constant Summary collapse

BASE_URL = 
'http://resource.belframework.org/belframework/latest-release'
DEFAULT_NAMESPACES = 
{
  'AFFX' =>
    BELParser::Expression::Model::Namespace.new(
      'AFFX',
      'http://www.openbel.org/bel/namespace/affy-probeset',
      "#{BASE_URL}/namespace/affy-probeset-ids.belns"),
  'CHEBI' =>
    BELParser::Expression::Model::Namespace.new(
      'CHEBI',
      'http://www.openbel.org/bel/namespace/chebi',
      "#{BASE_URL}/namespace/chebi.belns"),
  'CHEBIID' =>
    BELParser::Expression::Model::Namespace.new(
      'CHEBIID',
      'http://www.openbel.org/bel/namespace/chebi',
      "#{BASE_URL}/namespace/chebi-ids.belns"),
  'DEFAULT' =>
    BELParser::Expression::Model::Namespace.new(
      'DEFAULT',
      'http://www.openbel.org/bel/namespace/default',
      "#{BASE_URL}/namespace/default-bel-namespace.belns"),
  'DO' =>
    BELParser::Expression::Model::Namespace.new(
      'DO',
      'http://www.openbel.org/bel/namespace/disease-ontology',
      "#{BASE_URL}/namespace/disease-ontology.belns"),
  'DOID' =>
    BELParser::Expression::Model::Namespace.new(
      'DOID',
      'http://www.openbel.org/bel/namespace/disease-ontology',
      "#{BASE_URL}/namespace/disease-ontology-ids.belns"),
  'EGID' =>
    BELParser::Expression::Model::Namespace.new(
      'EGID',
      'http://www.openbel.org/bel/namespace/entrez-gene',
      "#{BASE_URL}/namespace/entrez-gene-ids.belns"),
  'GOBP' =>
    BELParser::Expression::Model::Namespace.new(
      'GOBP',
      'http://www.openbel.org/bel/namespace/go-biological-process',
      "#{BASE_URL}/namespace/go-biological-process.belns"),
  'GOBPID' =>
    BELParser::Expression::Model::Namespace.new(
      'GOBPID',
      'http://www.openbel.org/bel/namespace/go-biological-process',
      "#{BASE_URL}/namespace/go-biological-process-ids.belns"),
  'GOCC' =>
    BELParser::Expression::Model::Namespace.new(
      'GOCC',
      'http://www.openbel.org/bel/namespace/go-cellular-component',
      "#{BASE_URL}/namespace/go-cellular-component.belns"),
  'GOCCID' =>
    BELParser::Expression::Model::Namespace.new(
      'GOCCID',
      'http://www.openbel.org/bel/namespace/go-cellular-component',
      "#{BASE_URL}/namespace/go-cellular-component-ids.belns"),
  'HGNC' =>
    BELParser::Expression::Model::Namespace.new(
      'HGNC',
      'http://www.openbel.org/bel/namespace/hgnc-human-genes',
      "#{BASE_URL}/namespace/hgnc-human-genes.belns"),
  'MESHCS' =>
    BELParser::Expression::Model::Namespace.new(
      'MESHCS',
      'http://www.openbel.org/bel/namespace/mesh-cellular-structures',
      "#{BASE_URL}/namespace/mesh-cellular-structures.belns"),
  'MESHCSID' =>
    BELParser::Expression::Model::Namespace.new(
      'MESHCSID',
      'http://www.openbel.org/bel/namespace/mesh-cellular-structures',
      "#{BASE_URL}/namespace/mesh-cellular-structures-ids.belns"),
  'MESHC' =>
    BELParser::Expression::Model::Namespace.new(
      'MESHC',
      'http://www.openbel.org/bel/namespace/mesh-chemicals',
      "#{BASE_URL}/namespace/mesh-chemicals.belns"),
  'MESHCID' =>
    BELParser::Expression::Model::Namespace.new(
      'MESHCID',
      'http://www.openbel.org/bel/namespace/mesh-chemicals',
      "#{BASE_URL}/namespace/mesh-chemicals-ids.belns"),
  'MESHD' =>
    BELParser::Expression::Model::Namespace.new(
      'MESHD',
      'http://www.openbel.org/bel/namespace/mesh-diseases',
      "#{BASE_URL}/namespace/mesh-diseases.belns"),
  'MESHDID' =>
    BELParser::Expression::Model::Namespace.new(
      'MESHDID',
      'http://www.openbel.org/bel/namespace/mesh-diseases',
      "#{BASE_URL}/namespace/mesh-diseases-ids.belns"),
  'MESHPP' =>
    BELParser::Expression::Model::Namespace.new(
      'MESHPP',
      'http://www.openbel.org/bel/namespace/mesh-processes',
      "#{BASE_URL}/namespace/mesh-processes.belns"),
  'MESHPPID' =>
    BELParser::Expression::Model::Namespace.new(
      'MESHPPID',
      'http://www.openbel.org/bel/namespace/mesh-processes',
      "#{BASE_URL}/namespace/mesh-processes-ids.belns"),
  'MGI' =>
    BELParser::Expression::Model::Namespace.new(
      'MGI',
      'http://www.openbel.org/bel/namespace/mgi-mouse-genes',
      "#{BASE_URL}/namespace/mgi-mouse-genes.belns"),
  'RGD' =>
    BELParser::Expression::Model::Namespace.new(
      'RGD',
      'http://www.openbel.org/bel/namespace/rgd-rat-genes',
      "#{BASE_URL}/namespace/rgd-rat-genes.belns"),
  'SCHEM' =>
    BELParser::Expression::Model::Namespace.new(
      'SCHEM',
      'http://www.openbel.org/bel/namespace/selventa-legacy-chemicals',
      "#{BASE_URL}/namespace/selventa-legacy-chemicals.belns"),
  'SCOMP' =>
    BELParser::Expression::Model::Namespace.new(
      'SCOMP',
      'http://www.openbel.org/bel/namespace/selventa-named-complexes',
      "#{BASE_URL}/namespace/selventa-named-complexes.belns"),
  'SDIS' =>
    BELParser::Expression::Model::Namespace.new(
      'SDIS',
      'http://www.openbel.org/bel/namespace/selventa-legacy-diseases',
      "#{BASE_URL}/namespace/selventa-legacy-diseases"),
  'SFAM' =>
    BELParser::Expression::Model::Namespace.new(
      'SFAM',
      'http://www.openbel.org/bel/namespace/selventa-protein-families',
      "#{BASE_URL}/namespace/selventa-protein-families.belns"),
  'SP' =>
    BELParser::Expression::Model::Namespace.new(
      'SP',
      'http://www.openbel.org/bel/namespace/swissprot',
      "#{BASE_URL}/namespace/swissprot.belns"),
  'SPID' =>
    BELParser::Expression::Model::Namespace.new(
      'SPID',
      'http://www.openbel.org/bel/namespace/swissprot',
      "#{BASE_URL}/namespace/swissprot-ids.belns"),
}
DEFAULT_ANNOTATIONS = 
{
  'Anatomy' =>
    BELParser::Expression::Model::Namespace.new(
      'Anatomy',
      'http://www.openbel.org/bel/namespace/uberon',
      "#{BASE_URL}/annotation/anatomy.belanno"),
  'Cell' =>
    BELParser::Expression::Model::Namespace.new(
      'Cell',
      'http://www.openbel.org/bel/namespace/cell-ontology',
      "#{BASE_URL}/annotation/cell.belanno"),
  'CellLine' =>
    BELParser::Expression::Model::Namespace.new(
      'CellLine',
      'http://www.openbel.org/bel/namespace/cell-line-ontology',
      "#{BASE_URL}/annotation/cell-line.belanno"),
  'Disease' =>
    BELParser::Expression::Model::Namespace.new(
      'Disease',
      'http://www.openbel.org/bel/namespace/disease-ontology',
      "#{BASE_URL}/annotation/disease.belanno"),
  'ExperimentalFactor' =>
    BELParser::Expression::Model::Namespace.new(
      'ExperimentalFactor',
      'http://www.openbel.org/bel/namespace/experimental-factor-ontology',
      "#{BASE_URL}/annotation/disease.belanno"),
  'MeSHAnatomy' =>
    BELParser::Expression::Model::Namespace.new(
      'MeSHAnatomy',
      'http://www.openbel.org/bel/namespace/mesh-anatomy',
      "#{BASE_URL}/annotation/mesh-anatomy.belanno"),
  'MeSHDisease' =>
    BELParser::Expression::Model::Namespace.new(
      'MeSHDisease',
      'http://www.openbel.org/bel/namespace/mesh-diseases',
      "#{BASE_URL}/annotation/mesh-diseases.belanno"),
  'Species' =>
    BELParser::Expression::Model::Namespace.new(
      'Species',
      'http://www.openbel.org/bel/namespace/ncbi-taxonomy',
      "#{BASE_URL}/annotation/species-taxonomy-id.belanno")
}

Class Method Summary collapse

Class Method Details

.included(another_class) ⇒ Object 



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# File 'lib/bel_parser/resources.rb', line 192

def self.included(another_class)
  DEFAULT_ANNOTATIONS.each do |keyword, annotation|
    another_class.const_set(keyword.to_sym, annotation)
  end
  DEFAULT_NAMESPACES.each do |keyword, namespace|
    another_class.const_set(keyword.to_sym, namespace)
  end
end