Module: BEL::RDF

Defined in:
lib/bel/extensions/rdf/bel_rdf.rb

Constant Summary collapse

BELR =

uri prefixes

RUBYRDF::Vocabulary.new('http://www.openbel.org/bel/')
BELV = 
RUBYRDF::Vocabulary.new('http://www.openbel.org/vocabulary/')
PUBMED = 
RUBYRDF::Vocabulary.new('http://bio2rdf.org/pubmed:')
RDF = 
RUBYRDF
RDFS = 
RUBYRDF::RDFS
Anatomy =

annotations

RUBYRDF::Vocabulary.new('http://www.openbel.org/bel/annotation/anatomy/')
Cell = 
RUBYRDF::Vocabulary.new('http://www.openbel.org/bel/annotation/cell/')
CellLine = 
RUBYRDF::Vocabulary.new('http://www.openbel.org/bel/annotation/cell-line/')
CellStructure = 
RUBYRDF::Vocabulary.new('http://www.openbel.org/bel/annotation/cell-structure/')
Disease = 
RUBYRDF::Vocabulary.new('http://www.openbel.org/bel/annotation/disease/')
MeSHAnatomy = 
RUBYRDF::Vocabulary.new('http://www.openbel.org/bel/annotation/mesh-anatomy/')
MeSHDisease = 
RUBYRDF::Vocabulary.new('http://www.openbel.org/bel/annotation/mesh-diseases/')
Species = 
RUBYRDF::Vocabulary.new('http://www.openbel.org/bel/annotation/species-taxonomy-id/')
FUNCTION_TYPE =

maps outer function to bel/vocabulary class

{
  a:                       BELV.Abundance,
  act:                     BELV.AbundanceActivity,
  bp:                      BELV.BiologicalProcess,
  cat:                     BELV.AbundanceActivity,
  chap:                    BELV.AbundanceActivity,
  complex:                 BELV.ComplexAbundance,
  composite:               BELV.CompositeAbundance,
  deg:                     BELV.Degradation,
  fus:                     BELV.Fusion,
  g:                       BELV.GeneAbundance,
  gtp:                     BELV.AbundanceActivity,
  kin:                     BELV.AbundanceActivity,
  m:                       BELV.microRNAAbundance,
  p:                       BELV.ProteinAbundance,
  path:                    BELV.Pathology,
  pep:                     BELV.AbundanceActivity,
  phos:                    BELV.AbundanceActivity,
  pmod:                    BELV.ProteinModification,
  r:                       BELV.RNAAbundance,
  ribo:                    BELV.AbundanceActivity,
  rxn:                     BELV.Reaction,
  sec:                     BELV.CellSecretion,
  sub:                     BELV.Substitution,
  surf:                    BELV.CellSurfaceExpression,
  tloc:                    BELV.Translocation,
  tport:                   BELV.AbundanceActivity,
  tscript:                 BELV.AbundanceActivity,
  abundance:               BELV.Abundance,
  biologicalProcess:       BELV.BiologicalProcess,
  catalyticActivity:       BELV.AbundanceActivity,
  cellSecretion:           BELV.CellSecretion,
  cellSurfaceExpression:   BELV.CellSurfaceExpression,
  chaperoneActivity:       BELV.AbundanceActivity,
  complexAbundance:        BELV.ComplexAbundance,
  compositeAbundance:      BELV.CompositeAbundance,
  degradation:             BELV.Degradation,
  fusion:                  BELV.Fusion,
  geneAbundance:           BELV.GeneAbundance,
  gtpBoundActivity:        BELV.AbundanceActivity,
  kinaseActivity:          BELV.AbundanceActivity,
  list:                    BELV.List,
  microRNAAbundance:       BELV.microRNAAbundance,
  molecularActivity:       BELV.AbundanceActivity,
  pathology:               BELV.Pathology,
  peptidaseActivity:       BELV.AbundanceActivity,
  phosphataseActivity:     BELV.AbundanceActivity,
  products:                BELV.Products,
  proteinAbundance:        BELV.ProteinAbundance,
  proteinModification:     BELV.ProteinModification,
  reactants:               BELV.Reactants,
  reaction:                BELV.Reaction,
  ribosylationActivity:    BELV.AbundanceActivity,
  rnaAbundance:            BELV.RNAAbundance,
  substitution:            BELV.Substitution,
  transcriptionalActivity: BELV.AbundanceActivity,
  translocation:           BELV.Translocation,
  transportActivity:       BELV.AbundanceActivity,
  truncation:              BELV.Truncation,
}
RELATIONSHIP_TYPE = 
{
    '--'                     => BELV.Association,
    '-|'                     => BELV.Decreases,
    '=|'                     => BELV.DirectlyDecreases,
    '=>'                     => BELV.DirectlyIncreases,
    '->'                     => BELV.Increases,
    ':>'                     => BELV.TranscribedTo,
    '>>'                     => BELV.TranslatedTo,
    'actsIn'                 => BELV.ActsIn,
    'analogous'              => BELV.Analogous,
    'association'            => BELV.Association,
    'biomarkerFor'           => BELV.BiomarkerFor,
    'causesNoChange'         => BELV.CausesNoChange,
    'decreases'              => BELV.Decreases,
    'directlyDecreases'      => BELV.DirectlyDecreases,
    'directlyIncreases'      => BELV.DirectlyIncreases,
    'hasComponent'           => BELV.HasComponent,
    'hasComponents'          => BELV.HasComponents,
    'hasMember'              => BELV.HasMember,
    'hasMembers'             => BELV.HasMembers,
    'hasModification'        => BELV.HasModification,
    'hasProduct'             => BELV.HasProduct,
    'hasVariant'             => BELV.HasVariant,
    'includes'               => BELV.Includes,
    'increases'              => BELV.Increases,
    'isA'                    => BELV.IsA,
    'negativeCorrelation'    => BELV.NegativeCorrelation,
    'orthologous'            => BELV.Orthologous,
    'positiveCorrelation'    => BELV.PositiveCorrelation,
    'prognosticBiomarkerFor' => BELV.PrognosticBiomarkerFor,
    'rateLimitingStepOf'     => BELV.RateLimitingStepOf,
    'reactantIn'             => BELV.ReactantIn,
    'subProcessOf'           => BELV.SubProcessOf,
    'transcribedTo'          => BELV.TranscribedTo,
    'translatedTo'           => BELV.TranslatedTo,
    'translocates'           => BELV.Translocates,
}
RELATIONSHIP_CLASSIFICATION = 
{
    :'--'                     => BELV.CorrelativeRelationship,
    :'-|'                     => BELV.Decreases,
    :'=|'                     => BELV.DirectlyDecreases,
    :'=>'                     => BELV.DirectlyIncreases,
    :'->'                     => BELV.Increases,
    :'association'            => BELV.CorrelativeRelationship,
    :'biomarkerFor'           => BELV.BiomarkerFor,
    :'causesNoChange'         => BELV.CausesNoChange,
    :'decreases'              => BELV.Decreases,
    :'directlyDecreases'      => BELV.DirectlyDecreases,
    :'directlyIncreases'      => BELV.DirectlyIncreases,
    :'hasComponent'           => BELV.HasComponent,
    :'hasMember'              => BELV.HasMember,
    :'increases'              => BELV.Increases,
    :'isA'                    => BELV.IsA,
    :'negativeCorrelation'    => BELV.NegativeCorrelation,
    :'positiveCorrelation'    => BELV.PositiveCorrelation,
    :'prognosticBiomarkerFor' => BELV.PrognosticBiomarkerFor,
    :'rateLimitingStepOf'     => BELV.RateLimitingStepOf,
    :'subProcessOf'           => BELV.SubProcessOf,
}
ACTIVITY_TYPE = 
{
  act:                     BELV.Activity,
  cat:                     BELV.Catalytic,
  chap:                    BELV.Chaperone,
  gtp:                     BELV.GtpBound,
  kin:                     BELV.Kinase,
  pep:                     BELV.Peptidase,
  phos:                    BELV.Phosphatase,
  ribo:                    BELV.Ribosylase,
  tport:                   BELV.Transport,
  tscript:                 BELV.Transcription,
  catalyticActivity:       BELV.Catalytic,
  chaperoneActivity:       BELV.Chaperone,
  gtpBoundActivity:        BELV.GtpBound,
  kinaseActivity:          BELV.Kinase,
  molecularActivity:       BELV.Activity,
  peptidaseActivity:       BELV.Peptidase,
  phosphataseActivity:     BELV.Phosphatase,
  ribosylationActivity:    BELV.Ribosylase,
  transcriptionalActivity: BELV.Transcription,
  transportActivity:       BELV.Transport,
}
MODIFICATION_TYPE =

maps modification types to bel/vocabulary class

{
  'A'   => BELV.Acetylation,
  'F'   => BELV.Farnesylation,
  'G'   => BELV.Glycosylation,
  'H'   => BELV.Hydroxylation,
  'M'   => BELV.Methylation,
  'P'   => BELV.Phosphorylation,
  'P,S' => BELV.PhosphorylationSerine,
  'P,T' => BELV.PhosphorylationThreonine,
  'P,Y' => BELV.PhosphorylationTyrosine,
  'R'   => BELV.Ribosylation,
  'S'   => BELV.Sumoylation,
  'U'   => BELV.Ubiquitination,
}
PROTEIN_VARIANT =

protein variant

[:fus, :fusion, :sub, :substitution, :trunc, :truncation]

Class Method Summary collapse

Class Method Details

.vocabulary_rdf ⇒ Object 



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# File 'lib/bel/extensions/rdf/bel_rdf.rb', line 192

def self.vocabulary_rdf
  [
    # Classes
      # Concept - Annotations
      [BELV.AnnotationConcept, RDF::RDFS.subClassOf, RDF::SKOS.Concept],
      [BELV.AnnotationConceptScheme, RDF::RDFS.subClassOf, RDF::SKOS.ConceptScheme],
      # Concept - Namespaces
      [BELV.AbundanceConcept, RDF::RDFS.subClassOf, BELV.NamespaceConcept],
      [BELV.BiologicalProcessConcept, RDF::RDFS.subClassOf, BELV.NamespaceConcept],
      [BELV.ComplexConcept, RDF::RDFS.subClassOf, BELV.AbundanceConcept],
      [BELV.GeneConcept, RDF::RDFS.subClassOf, BELV.AbundanceConcept],
      [BELV.MicroRNAConcept, RDF::RDFS.subClassOf, BELV.RNAConcept],
      [BELV.NamespaceConceptScheme, RDF::RDFS.subClassOf, RDF::SKOS.ConceptScheme],
      [BELV.NamespaceConcept, RDF::RDFS.subClassOf, RDF::SKOS.Concept],
      [BELV.ProteinConcept, RDF::RDFS.subClassOf, BELV.AbundanceConcept],
      [BELV.RNAConcept, RDF::RDFS.subClassOf, BELV.AbundanceConcept],
      [BELV.PathologyConcept, RDF::RDFS.subClassOf, BELV.BiologicalProcessConcept],
      # BEL Language
      [BELV.Abundance, RDF.type, RDF::RDFS.Class],
      [BELV.Activity, RDF.type, RDF::RDFS.Class],
      [BELV.Evidence, RDF.type, RDF::RDFS.Class],
      [BELV.Modification, RDF.type, RDF::RDFS.Class],
      [BELV.Relationship, RDF.type, RDF::RDFS.Class],
      [BELV.Statement, RDF.type, RDF::RDFS.Class],
      [BELV.Term, RDF.type, RDF::RDFS.Class],
      # Relationships
      [BELV.Association, RDF::RDFS.subClassOf, BELV.CorrelativeRelationship],
      [BELV.BiomarkerFor, RDF::RDFS.subClassOf, BELV.Relationship],
      [BELV.CausesNoChange, RDF::RDFS.subClassOf, BELV.CausalRelationship],
      [BELV.CausalRelationship, RDF::RDFS.subClassOf, BELV.Relationship],
      [BELV.CorrelativeRelationship, RDF::RDFS.subClassOf, BELV.Relationship],
      [BELV.Decreases, RDF::RDFS.subClassOf, BELV.CausalRelationship],
      [BELV.Decreases, RDF::RDFS.subClassOf, BELV.NegativeRelationship],
      [BELV.DirectlyDecreases, RDF::RDFS.subClassOf, BELV.CausalRelationship],
      [BELV.DirectlyDecreases, RDF::RDFS.subClassOf, BELV.NegativeRelationship],
      [BELV.DirectlyDecreases, RDF::RDFS.subClassOf, BELV.DirectRelationship],
      [BELV.DirectlyDecreases, RDF::RDFS.subClassOf, BELV.Decreases],
      [BELV.DirectlyIncreases, RDF::RDFS.subClassOf, BELV.CausalRelationship],
      [BELV.DirectlyIncreases, RDF::RDFS.subClassOf, BELV.PositiveRelationship],
      [BELV.DirectlyIncreases, RDF::RDFS.subClassOf, BELV.DirectRelationship],
      [BELV.DirectlyIncreases, RDF::RDFS.subClassOf, BELV.Increases],
      [BELV.DirectRelationship, RDF::RDFS.subClassOf, BELV.Relationship],
      [BELV.HasComponent, RDF::RDFS.subClassOf, BELV.MembershipRelationship],
      [BELV.HasMember, RDF::RDFS.subClassOf, BELV.MembershipRelationship],
      [BELV.Increases, RDF::RDFS.subClassOf, BELV.CausalRelationship],
      [BELV.Increases, RDF::RDFS.subClassOf, BELV.PositiveRelationship],
      [BELV.IsA, RDF::RDFS.subClassOf, BELV.MembershipRelationship],
      [BELV.MembershipRelationship, RDF::RDFS.subClassOf, BELV.Relationship],
      [BELV.NegativeCorrelation, RDF::RDFS.subClassOf, BELV.CorrelativeRelationship],
      [BELV.NegativeCorrelation, RDF::RDFS.subClassOf, BELV.NegativeRelationship],
      [BELV.NegativeRelationship, RDF::RDFS.subClassOf, BELV.Relationship],
      [BELV.PositiveCorrelation, RDF::RDFS.subClassOf, BELV.CorrelativeRelationship],
      [BELV.PositiveCorrelation, RDF::RDFS.subClassOf, BELV.PositiveRelationship],
      [BELV.PositiveRelationship, RDF::RDFS.subClassOf, BELV.Relationship],
      [BELV.PrognosticBiomarkerFor, RDF::RDFS.subClassOf, BELV.BiomarkerFor],
      [BELV.RateLimitingStepOf, RDF::RDFS.subClassOf, BELV.Increases],
      [BELV.RateLimitingStepOf, RDF::RDFS.subClassOf, BELV.CausalRelationship],
      [BELV.RateLimitingStepOf, RDF::RDFS.subClassOf, BELV.SubProcessOf],
      [BELV.SubProcessOf, RDF::RDFS.subClassOf, BELV.MembershipRelationship],
      # Abundances
      [BELV.AbundanceActivity, RDF::RDFS.subClassOf, BELV.Process],
      [BELV.BiologicalProcess, RDF::RDFS.subClassOf, BELV.Process],
      [BELV.CellSecretion, RDF::RDFS.subClassOf, BELV.Translocation],
      [BELV.ComplexAbundance, RDF::RDFS.subClassOf, BELV.Abundance],
      [BELV.CompositeAbundance, RDF::RDFS.subClassOf, BELV.Abundance],
      [BELV.Degradation, RDF::RDFS.subClassOf, BELV.Transformation],
      [BELV.GeneAbundance, RDF::RDFS.subClassOf, BELV.Abundance],
      [BELV.MicroRNAAbundance, RDF::RDFS.subClassOf, BELV.Abundance],
      [BELV.ModifiedProteinAbundance, RDF::RDFS.subClassOf, BELV.ProteinAbundance],
      [BELV.Pathology, RDF::RDFS.subClassOf, BELV.BiologicalProcess],
      [BELV.Process, RDF.type, RDF::RDFS.Class],
      [BELV.ProteinAbundance, RDF::RDFS.subClassOf, BELV.Abundance],
      [BELV.ProteinVariantAbundance, RDF::RDFS.subClassOf, BELV.ProteinAbundance],
      [BELV.Reaction, RDF::RDFS.subClassOf, BELV.Transformation],
      [BELV.RNAAbundance, RDF::RDFS.subClassOf, BELV.Abundance],
      [BELV.Transformation, RDF::RDFS.subClassOf, BELV.Process],
      [BELV.Translocation, RDF::RDFS.subClassOf, BELV.Transformation],
      # Activities
      [BELV.Activity, RDF::RDFS.subClassOf, BELV.Activity],
      [BELV.Catalytic, RDF::RDFS.subClassOf, BELV.Activity],
      [BELV.Chaperone, RDF::RDFS.subClassOf, BELV.Activity],
      [BELV.GtpBound, RDF::RDFS.subClassOf, BELV.Activity],
      [BELV.Kinase, RDF::RDFS.subClassOf, BELV.Activity],
      [BELV.Peptidase, RDF::RDFS.subClassOf, BELV.Activity],
      [BELV.Phosphatase, RDF::RDFS.subClassOf, BELV.Activity],
      [BELV.Ribosylase, RDF::RDFS.subClassOf, BELV.Activity],
      [BELV.Transcription, RDF::RDFS.subClassOf, BELV.Activity],
      [BELV.Transport, RDF::RDFS.subClassOf, BELV.Activity],
      # Modifications
      [BELV.Acetylation, RDF::RDFS.subClassOf, BELV.Modification],
      [BELV.Farnesylation, RDF::RDFS.subClassOf, BELV.Modification],
      [BELV.Glycosylation, RDF::RDFS.subClassOf, BELV.Modification],
      [BELV.Hydroxylation, RDF::RDFS.subClassOf, BELV.Modification],
      [BELV.Methylation, RDF::RDFS.subClassOf, BELV.Modification],
      [BELV.Phosphorylation, RDF::RDFS.subClassOf, BELV.Modification],
      [BELV.Ribosylation, RDF::RDFS.subClassOf, BELV.Modification],
      [BELV.Sumoylation, RDF::RDFS.subClassOf, BELV.Modification],
      [BELV.Ubiquitination, RDF::RDFS.subClassOf, BELV.Modification],
      [BELV.PhosphorylationSerine, RDF::RDFS.subClassOf, BELV.Phosphorylation],
      [BELV.PhosphorylationTyrosine, RDF::RDFS.subClassOf, BELV.Phosphorylation],
      [BELV.PhosphorylationThreonine, RDF::RDFS.subClassOf, BELV.Phosphorylation],

    # Properties
      # Term
      [BELV.hasActivityType, RDF.type, RDF.Property],
      [BELV.hasActivityType, RDF::RDFS.range, BELV.Activity],
      [BELV.hasActivityType, RDF::RDFS.domain, BELV.Term],
      [BELV.hasChild, RDF.type, RDF.Property],
      [BELV.hasChild, RDF::RDFS.range, BELV.Term],
      [BELV.hasChild, RDF::RDFS.domain, BELV.Term],
      [BELV.hasConcept, RDF.type, RDF.Property],
      [BELV.hasConcept, RDF::RDFS.range, BELV.NamespaceConcept],
      [BELV.hasConcept, RDF::RDFS.domain, BELV.Term],
      [BELV.hasModificationPosition, RDF.type, RDF.Property],
      [BELV.hasModificationPosition, RDF::RDFS.range, RDF::XSD.integer],
      [BELV.hasModificationPosition, RDF::RDFS.domain, BELV.Term],
      [BELV.hasModificationType, RDF.type, RDF.Property],
      [BELV.hasModificationType, RDF::RDFS.range, BELV.Activity],
      [BELV.hasModificationType, RDF::RDFS.domain, BELV.Term],
      # Statement
      [BELV.hasEvidence, RDF.type, RDF.Property],
      [BELV.hasEvidence, RDF::RDFS.range, BELV.Evidence],
      [BELV.hasEvidence, RDF::RDFS.domain, BELV.Statement],
      [BELV.hasObject, RDF::RDFS.subPropertyOf, BELV.hasChild],
      [BELV.hasObject, RDF::RDFS.range, BELV.Term],
      [BELV.hasObject, RDF::RDFS.domain, BELV.Statement],
      [BELV.hasRelationship, RDF.type, RDF.Property],
      [BELV.hasRelationship, RDF::RDFS.range, BELV.Relationship],
      [BELV.hasRelationship, RDF::RDFS.domain, BELV.Statement],
      [BELV.hasSubject, RDF::RDFS.subPropertyOf, BELV.hasChild],
      [BELV.hasSubject, RDF::RDFS.range, BELV.Term],
      [BELV.hasSubject, RDF::RDFS.domain, BELV.Statement],
      # Evidence
      [BELV.hasAnnotation, RDF.type, RDF.Property],
      [BELV.hasAnnotation, RDF::RDFS.range, BELV.AnnotationConcept],
      [BELV.hasAnnotation, RDF::RDFS.domain, BELV.Evidence],
      [BELV.hasCitation, RDF.type, RDF.Property],
      [BELV.hasCitation, RDF::RDFS.domain, BELV.Evidence],
      [BELV.hasEvidenceText, RDF::RDFS.range, RDF::XSD.string],
      [BELV.hasEvidenceText, RDF::RDFS.domain, BELV.Evidence],
      [BELV.hasStatement, RDF.type, RDF.Property],
      [BELV.hasStatement, RDF::RDFS.range, BELV.Statement],
      [BELV.hasStatement, RDF::RDFS.domain, BELV.Evidence]
  ]
end