Module: BEL::Namespace

Included in:

Translator::Plugins::Jgf::JgfTranslator

Defined in:

lib/bel/namespace.rb

Defined Under Namespace

Classes: NamespaceDefinition, ResourceIndex

Constant Summary

LATEST_PREFIX =

'http://resource.belframework.org/belframework/latest-release/'

DEFAULT_URI =

'http://www.openbel.org/bel/namespace/'

NAMESPACE_LATEST =

{
  AFFX: [
    LATEST_PREFIX + 'namespace/affy-probeset-ids.belns',
    'http://www.openbel.org/bel/namespace/affy-probeset'
  ],
  CHEBI: [
    LATEST_PREFIX + 'namespace/chebi.belns',
    'http://www.openbel.org/bel/namespace/chebi'
  ],
  CHEBIID: [
    LATEST_PREFIX + 'namespace/chebi-ids.belns',
    'http://www.openbel.org/bel/namespace/chebi'
  ],
  DO: [
    LATEST_PREFIX + 'namespace/disease-ontology.belns',
    'http://www.openbel.org/bel/namespace/disease-ontology'
  ],
  DOID: [
    LATEST_PREFIX + 'namespace/disease-ontology-ids.belns',
    'http://www.openbel.org/bel/namespace/disease-ontology'
  ],
  EGID: [
    LATEST_PREFIX + 'namespace/entrez-gene-ids.belns',
    'http://www.openbel.org/bel/namespace/entrez-gene'
  ],
  GOBP: [
    LATEST_PREFIX + 'namespace/go-biological-process.belns',
    'http://www.openbel.org/bel/namespace/go-biological-process'
  ],
  GOBPID: [
    LATEST_PREFIX + 'namespace/go-biological-process-ids.belns',
    'http://www.openbel.org/bel/namespace/go-biological-process'
  ],
  GOCC: [
    LATEST_PREFIX + 'namespace/go-cellular-component.belns',
    'http://www.openbel.org/bel/namespace/go-cellular-component'
  ],
  GOCCID: [
    LATEST_PREFIX + 'namespace/go-cellular-component-ids.belns',
    'http://www.openbel.org/bel/namespace/go-cellular-component'
  ],
  HGNC: [
    LATEST_PREFIX + 'namespace/hgnc-human-genes.belns',
    'http://www.openbel.org/bel/namespace/hgnc-human-genes'
  ],
  MESHCS: [
    LATEST_PREFIX + 'namespace/mesh-cellular-structures.belns',
    'http://www.openbel.org/bel/namespace/mesh-cellular-structures'
  ],
  MESHCSID: [
    LATEST_PREFIX + 'namespace/mesh-cellular-structures-ids.belns',
    'http://www.openbel.org/bel/namespace/mesh-cellular-structures'
  ],
  MECHC: [
    LATEST_PREFIX + 'namespace/mesh-chemicals.belns',
    'http://www.openbel.org/bel/namespace/mesh-chemicals'
  ],
  MECHCID: [
    LATEST_PREFIX + 'namespace/mesh-chemicals-ids.belns',
    'http://www.openbel.org/bel/namespace/mesh-chemicals'
  ],
  MESHD: [
    LATEST_PREFIX + 'namespace/mesh-diseases.belns',
    'http://www.openbel.org/bel/namespace/mesh-diseases',
  ],
  MESHDID: [
    LATEST_PREFIX + 'namespace/mesh-diseases-ids.belns',
    'http://www.openbel.org/bel/namespace/mesh-diseases',
  ],
  MESHPP: [
    LATEST_PREFIX + 'namespace/mesh-processes.belns',
    'http://www.openbel.org/bel/namespace/mesh-processes'
  ],
  MESHPPID: [
    LATEST_PREFIX + 'namespace/mesh-processes-ids.belns',
    'http://www.openbel.org/bel/namespace/mesh-processes'
  ],
  MGI: [
    LATEST_PREFIX + 'namespace/mgi-mouse-genes.belns',
    'http://www.openbel.org/bel/namespace/mgi-mouse-genes'
  ],
  RGD: [
    LATEST_PREFIX + 'namespace/rgd-rat-genes.belns',
    'http://www.openbel.org/bel/namespace/rgd-rat-genes'
  ],
  SCOMP: [
    LATEST_PREFIX + 'namespace/selventa-named-complexes.belns',
    'http://www.openbel.org/bel/namespace/selventa-named-complexes'
  ],
  SCHEM: [
    LATEST_PREFIX + 'namespace/selventa-legacy-chemicals.belns',
    'http://www.openbel.org/bel/namespace/selventa-legacy-chemicals'
  ],
  SDIS: [
    LATEST_PREFIX + 'namespace/selventa-legacy-diseases.belns',
    'http://www.openbel.org/bel/namespace/selventa-legacy-diseases'
  ],
  SFAM: [
    LATEST_PREFIX + 'namespace/selventa-protein-families.belns',
    'http://www.openbel.org/bel/namespace/selventa-protein-families'
  ],
  SP: [
    LATEST_PREFIX + 'namespace/swissprot.belns',
    'http://www.openbel.org/bel/namespace/swissprot'
  ],
  SPID: [
    LATEST_PREFIX + 'namespace/swissprot-ids.belns',
    'http://www.openbel.org/bel/namespace/swissprot'
  ]
}

NAMESPACE_BELNS =

XXX 1.0 namespaces without rdf support

{
  HGU95AV2:  'http://resource.belframework.org/belframework/1.0/namespace/affy-hg-u95av2.belns',
  HGU133P2:  'http://resource.belframework.org/belframework/1.0/namespace/affy-hg-u133-plus2.belns',
  HGU133AB:  'http://resource.belframework.org/belframework/1.0/namespace/affy-hg-u133ab.belns',
  MGU74ABC:  'http://resource.belframework.org/belframework/1.0/namespace/affy-mg-u74abc.belns',
  MG430AB:   'http://resource.belframework.org/belframework/1.0/namespace/affy-moe430ab.belns',
  MG4302:    'http://resource.belframework.org/belframework/1.0/namespace/affy-mouse430-2.belns',
  MG430A2:   'http://resource.belframework.org/belframework/1.0/namespace/affy-mouse430a-2.belns',
  RG230AB:   'http://resource.belframework.org/belframework/1.0/namespace/affy-rae230ab-2.belns',
  RG2302:    'http://resource.belframework.org/belframework/1.0/namespace/affy-rat230-2.belns',
  CHEBIID:   'http://resource.belframework.org/belframework/1.0/namespace/chebi-ids.belns',
  CHEBI:     'http://resource.belframework.org/belframework/1.0/namespace/chebi-names.belns',
  EGID:      'http://resource.belframework.org/belframework/1.0/namespace/entrez-gene-ids-hmr.belns',
  GOAC:      'http://resource.belframework.org/belframework/1.0/namespace/go-biological-processes-accession-numbers.belns',
  GO:        'http://resource.belframework.org/belframework/1.0/namespace/go-biological-processes-names.belns',
  GOCCACC:   'http://resource.belframework.org/belframework/1.0/namespace/go-cellular-component-accession-numbers.belns',
  GOCCTERM:  'http://resource.belframework.org/belframework/1.0/namespace/go-cellular-component-terms.belns',
  HGNC:      'http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns',
  MESHPP:    'http://resource.belframework.org/belframework/1.0/namespace/mesh-biological-processes.belns',
  MESHCL:    'http://resource.belframework.org/belframework/1.0/namespace/mesh-cellular-locations.belns',
  MESHD:     'http://resource.belframework.org/belframework/1.0/namespace/mesh-diseases.belns',
  MGI:       'http://resource.belframework.org/belframework/1.0/namespace/mgi-approved-symbols.belns',
  RGD:       'http://resource.belframework.org/belframework/1.0/namespace/rgd-approved-symbols.belns',
  SCHEM:     'http://resource.belframework.org/belframework/1.0/namespace/selventa-legacy-chemical-names.belns',
  SDIS:      'http://resource.belframework.org/belframework/1.0/namespace/selventa-legacy-diseases.belns',
  NCH:       'http://resource.belframework.org/belframework/1.0/namespace/selventa-named-human-complexes.belns',
  PFH:       'http://resource.belframework.org/belframework/1.0/namespace/selventa-named-human-protein-families.belns',
  NCM:       'http://resource.belframework.org/belframework/1.0/namespace/selventa-named-mouse-complexes.belns',
  PFM:       'http://resource.belframework.org/belframework/1.0/namespace/selventa-named-mouse-protein-families.belns',
  NCR:       'http://resource.belframework.org/belframework/1.0/namespace/selventa-named-rat-complexes.belns',
  PFR:       'http://resource.belframework.org/belframework/1.0/namespace/selventa-named-rat-protein-families.belns',
  SPAC:      'http://resource.belframework.org/belframework/1.0/namespace/swissprot-accession-numbers.belns',
  SP:        'http://resource.belframework.org/belframework/1.0/namespace/swissprot-entry-names.belns'
}

DEFAULT_NAMESPACES =

create classes for each standard prefix

NAMESPACE_LATEST.collect do |prefix, values|
  rdf_uri = NAMESPACE_LATEST[prefix][1] || DEFAULT_URI
  ns_definition = NamespaceDefinition.new(prefix, values[0], rdf_uri)
  Namespace.const_set(prefix, ns_definition)
  ns_definition
end