Module: BELRDF

Defined in:: lib/bel/translator/plugins/rdf/bel_schema.rb,
lib/bel/translator/plugins/rdf/uuid.rb,
lib/bel/translator/plugins/rdf/reader.rb,
lib/bel/translator/plugins/rdf/writer.rb,
lib/bel/translator/plugins/rdf/translator.rb,
lib/bel/translator/plugins/rdf/monkey_patch.rb,
lib/bel/translator/plugins/rdf/graph_translator.rb

Overview

Defines the RDF vocabulary for BEL structures.

Defined Under Namespace

Modules: Reader, Writer Classes: GraphTranslator, Translator

Constant Summary collapse

BELR = uri prefixes

::RDF::Vocabulary.new('http://www.openbel.org/bel/')

BELV =

::RDF::Vocabulary.new('http://www.openbel.org/vocabulary/')

BELE =

::RDF::Vocabulary.new('http://www.openbel.org/evidence/')

DC =

::RDF::Vocab::DC

FOAF =

::RDF::Vocab::FOAF

PUBMED =

::RDF::Vocabulary.new('http://bio2rdf.org/pubmed:')

RDF =

::RDF

RDFS =

::RDF::Vocab::RDFS

SKOS =

::RDF::Vocab::SKOS

VOID =

::RDF::Vocab::VOID

XSD =

::RDF::Vocab::XSD

Anatomy = annotations

'http://www.openbel.org/bel/annotation/anatomy/'

Cell =

'http://www.openbel.org/bel/annotation/cell/'

CellLine =

'http://www.openbel.org/bel/annotation/cell-line/'

CellStructure =

'http://www.openbel.org/bel/annotation/cell-structure/'

Disease =

'http://www.openbel.org/bel/annotation/disease/'

MeSHAnatomy =

'http://www.openbel.org/bel/annotation/mesh-anatomy/'

MeSHDisease =

'http://www.openbel.org/bel/annotation/mesh-diseases/'

Species =

'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]

RDFS_SCHEMA =

deep_freeze([
  # Classes - Annotation Concept
  [BELV.AnnotationConcept, RDFS.subClassOf, SKOS.Concept],
  [BELV.AnnotationConceptScheme, RDFS.subClassOf, SKOS.ConceptScheme],

  # Classes - Namespace Concept
  [BELV.AbundanceConcept, RDFS.subClassOf, BELV.NamespaceConcept],
  [BELV.BiologicalProcessConcept, RDFS.subClassOf, BELV.NamespaceConcept],
  [BELV.ComplexConcept, RDFS.subClassOf, BELV.AbundanceConcept],
  [BELV.GeneConcept, RDFS.subClassOf, BELV.AbundanceConcept],
  [BELV.MicroRNAConcept, RDFS.subClassOf, BELV.RNAConcept],
  [BELV.NamespaceConceptScheme, RDFS.subClassOf, SKOS.ConceptScheme],
  [BELV.NamespaceConcept, RDFS.subClassOf, SKOS.Concept],
  [BELV.ProteinConcept, RDFS.subClassOf, BELV.AbundanceConcept],
  [BELV.RNAConcept, RDFS.subClassOf, BELV.AbundanceConcept],
  [BELV.PathologyConcept, RDFS.subClassOf, BELV.BiologicalProcessConcept],

  # Classes - Language Concepts
  [BELV.Abundance, RDF.type, RDFS.Class],
  [BELV.Activity, RDF.type, RDFS.Class],
  [BELV.Nanopub, RDF.type, RDFS.Class],
  [BELV.Modification, RDF.type, RDFS.Class],
  [BELV.Relationship, RDF.type, RDFS.Class],
  [BELV.Statement, RDF.type, RDFS.Class],
  [BELV.Term, RDF.type, RDFS.Class],

  # Classes - Relationships
  [BELV.Association, RDFS.subClassOf, BELV.CorrelativeRelationship],
  [BELV.BiomarkerFor, RDFS.subClassOf, BELV.Relationship],
  [BELV.CausesNoChange, RDFS.subClassOf, BELV.CausalRelationship],
  [BELV.CausalRelationship, RDFS.subClassOf, BELV.Relationship],
  [BELV.CorrelativeRelationship, RDFS.subClassOf, BELV.Relationship],
  [BELV.Decreases, RDFS.subClassOf, BELV.CausalRelationship],
  [BELV.Decreases, RDFS.subClassOf, BELV.NegativeRelationship],
  [BELV.DirectlyDecreases, RDFS.subClassOf, BELV.CausalRelationship],
  [BELV.DirectlyDecreases, RDFS.subClassOf, BELV.NegativeRelationship],
  [BELV.DirectlyDecreases, RDFS.subClassOf, BELV.DirectRelationship],
  [BELV.DirectlyDecreases, RDFS.subClassOf, BELV.Decreases],
  [BELV.DirectlyIncreases, RDFS.subClassOf, BELV.CausalRelationship],
  [BELV.DirectlyIncreases, RDFS.subClassOf, BELV.PositiveRelationship],
  [BELV.DirectlyIncreases, RDFS.subClassOf, BELV.DirectRelationship],
  [BELV.DirectlyIncreases, RDFS.subClassOf, BELV.Increases],
  [BELV.DirectRelationship, RDFS.subClassOf, BELV.Relationship],
  [BELV.HasComponent, RDFS.subClassOf, BELV.MembershipRelationship],
  [BELV.HasMember, RDFS.subClassOf, BELV.MembershipRelationship],
  [BELV.Increases, RDFS.subClassOf, BELV.CausalRelationship],
  [BELV.Increases, RDFS.subClassOf, BELV.PositiveRelationship],
  [BELV.IsA, RDFS.subClassOf, BELV.MembershipRelationship],
  [BELV.MembershipRelationship, RDFS.subClassOf, BELV.Relationship],
  [BELV.NegativeCorrelation, RDFS.subClassOf, BELV.CorrelativeRelationship],
  [BELV.NegativeCorrelation, RDFS.subClassOf, BELV.NegativeRelationship],
  [BELV.NegativeRelationship, RDFS.subClassOf, BELV.Relationship],
  [BELV.PositiveCorrelation, RDFS.subClassOf, BELV.CorrelativeRelationship],
  [BELV.PositiveCorrelation, RDFS.subClassOf, BELV.PositiveRelationship],
  [BELV.PositiveRelationship, RDFS.subClassOf, BELV.Relationship],
  [BELV.PrognosticBiomarkerFor, RDFS.subClassOf, BELV.BiomarkerFor],
  [BELV.RateLimitingStepOf, RDFS.subClassOf, BELV.Increases],
  [BELV.RateLimitingStepOf, RDFS.subClassOf, BELV.CausalRelationship],
  [BELV.RateLimitingStepOf, RDFS.subClassOf, BELV.SubProcessOf],
  [BELV.SubProcessOf, RDFS.subClassOf, BELV.MembershipRelationship],

  # Classes - Abundances
  [BELV.AbundanceActivity, RDFS.subClassOf, BELV.Process],
  [BELV.BiologicalProcess, RDFS.subClassOf, BELV.Process],
  [BELV.CellSecretion, RDFS.subClassOf, BELV.Translocation],
  [BELV.ComplexAbundance, RDFS.subClassOf, BELV.Abundance],
  [BELV.CompositeAbundance, RDFS.subClassOf, BELV.Abundance],
  [BELV.Degradation, RDFS.subClassOf, BELV.Transformation],
  [BELV.GeneAbundance, RDFS.subClassOf, BELV.Abundance],
  [BELV.MicroRNAAbundance, RDFS.subClassOf, BELV.Abundance],
  [BELV.ModifiedProteinAbundance, RDFS.subClassOf, BELV.ProteinAbundance],
  [BELV.Pathology, RDFS.subClassOf, BELV.BiologicalProcess],
  [BELV.Process, RDF.type, RDFS.Class],
  [BELV.ProteinAbundance, RDFS.subClassOf, BELV.Abundance],
  [BELV.ProteinVariantAbundance, RDFS.subClassOf, BELV.ProteinAbundance],
  [BELV.Reaction, RDFS.subClassOf, BELV.Transformation],
  [BELV.RNAAbundance, RDFS.subClassOf, BELV.Abundance],
  [BELV.Transformation, RDFS.subClassOf, BELV.Process],
  [BELV.Translocation, RDFS.subClassOf, BELV.Transformation],

  # Classes - Activities
  [BELV.Activity, RDFS.subClassOf, BELV.Activity],
  [BELV.Catalytic, RDFS.subClassOf, BELV.Activity],
  [BELV.Chaperone, RDFS.subClassOf, BELV.Activity],
  [BELV.GtpBound, RDFS.subClassOf, BELV.Activity],
  [BELV.Kinase, RDFS.subClassOf, BELV.Activity],
  [BELV.Peptidase, RDFS.subClassOf, BELV.Activity],
  [BELV.Phosphatase, RDFS.subClassOf, BELV.Activity],
  [BELV.Ribosylase, RDFS.subClassOf, BELV.Activity],
  [BELV.Transcription, RDFS.subClassOf, BELV.Activity],
  [BELV.Transport, RDFS.subClassOf, BELV.Activity],

  # Classes - Modifications
  [BELV.Acetylation, RDFS.subClassOf, BELV.Modification],
  [BELV.Farnesylation, RDFS.subClassOf, BELV.Modification],
  [BELV.Glycosylation, RDFS.subClassOf, BELV.Modification],
  [BELV.Hydroxylation, RDFS.subClassOf, BELV.Modification],
  [BELV.Methylation, RDFS.subClassOf, BELV.Modification],
  [BELV.Phosphorylation, RDFS.subClassOf, BELV.Modification],
  [BELV.Ribosylation, RDFS.subClassOf, BELV.Modification],
  [BELV.Sumoylation, RDFS.subClassOf, BELV.Modification],
  [BELV.Ubiquitination, RDFS.subClassOf, BELV.Modification],
  [BELV.PhosphorylationSerine, RDFS.subClassOf, BELV.Phosphorylation],
  [BELV.PhosphorylationTyrosine, RDFS.subClassOf, BELV.Phosphorylation],
  [BELV.PhosphorylationThreonine, RDFS.subClassOf, BELV.Phosphorylation],

  # Properties - BEL Term
  [BELV.hasActivityType, RDF.type, RDF.Property],
  [BELV.hasActivityType, RDFS.range, BELV.Activity],
  [BELV.hasActivityType, RDFS.domain, BELV.Term],
  [BELV.hasChild, RDF.type, RDF.Property],
  [BELV.hasChild, RDFS.range, BELV.Term],
  [BELV.hasChild, RDFS.domain, BELV.Term],
  [BELV.hasConcept, RDF.type, RDF.Property],
  [BELV.hasConcept, RDFS.range, BELV.NamespaceConcept],
  [BELV.hasConcept, RDFS.domain, BELV.Term],
  [BELV.hasModificationPosition, RDF.type, RDF.Property],
  [BELV.hasModificationPosition, RDFS.range, XSD.integer],
  [BELV.hasModificationPosition, RDFS.domain, BELV.Term],
  [BELV.hasModificationType, RDF.type, RDF.Property],
  [BELV.hasModificationType, RDFS.range, BELV.Activity],
  [BELV.hasModificationType, RDFS.domain, BELV.Term],

  # Properties - BEL Statement
  [BELV.hasNanopub, RDF.type, RDF.Property],
  [BELV.hasNanopub, RDFS.range, BELV.Nanopub],
  [BELV.hasNanopub, RDFS.domain, BELV.Statement],
  [BELV.hasObject, RDFS.subPropertyOf, BELV.hasChild],
  [BELV.hasObject, RDFS.range, BELV.Term],
  [BELV.hasObject, RDFS.domain, BELV.Statement],
  [BELV.hasRelationship, RDF.type, RDF.Property],
  [BELV.hasRelationship, RDFS.range, BELV.Relationship],
  [BELV.hasRelationship, RDFS.domain, BELV.Statement],
  [BELV.hasSubject, RDFS.subPropertyOf, BELV.hasChild],
  [BELV.hasSubject, RDFS.range, BELV.Term],
  [BELV.hasSubject, RDFS.domain, BELV.Statement],

  # Properties - Nanopub
  [BELV.hasAnnotation, RDF.type, RDF.Property],
  [BELV.hasAnnotation, RDFS.range, BELV.AnnotationConcept],
  [BELV.hasAnnotation, RDFS.domain, BELV.Nanopub],
  [BELV.hasCitation, RDF.type, RDF.Property],
  [BELV.hasCitation, RDFS.domain, BELV.Nanopub],
  [BELV.hasNanopubText, RDFS.range, XSD.string],
  [BELV.hasNanopubText, RDFS.domain, BELV.Nanopub],
  [BELV.hasStatement, RDF.type, RDF.Property],
  [BELV.hasStatement, RDFS.range, BELV.Statement],
  [BELV.hasStatement, RDFS.domain, BELV.Nanopub]
])

Class Method Summary collapse

.vocabulary_rdf ⇒ Object

Class Method Details

.vocabulary_rdf ⇒ `Object`



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# File 'lib/bel/translator/plugins/rdf/bel_schema.rb', line 353

def self.vocabulary_rdf
  RDFS_SCHEMA
end