bel 0.7.0 → 1.0.0

data/lib/bel/translator/plugins/rdf/translator.rb

@@ -26,7 +26,7 @@ module BELRDF
     end
 
     def read(data, options = {})
-      Reader::UnbufferedEvidenceYielder.new(data, @format)
+      Reader::UnbufferedNanopubYielder.new(data, @format)
     end
 
     def write(objects, io = StringIO.new, options = {})
@@ -68,10 +68,10 @@ module BELRDF
           yielder << RDF::Statement.new(*schema_statement)
         end
 
-        # enumerate BEL evidence
-        objects.each do |evidence|
+        # enumerate BEL nanopubs
+        objects.each do |nanopub|
           if void_dataset_uri && !wrote_dataset
-            void_dataset_triples = evidence.to_void_dataset(void_dataset_uri)
+            void_dataset_triples = nanopub.to_void_dataset(void_dataset_uri)
             if void_dataset_triples && void_dataset_triples.respond_to?(:each)
               void_dataset_triples.each do |void_triple|
                 yielder << void_triple
@@ -80,7 +80,7 @@ module BELRDF
             wrote_dataset = true
           end
 
-          evidence_uri, statements = evidence.to_rdf(remap)
+          nanopub_uri, statements = nanopub.to_rdf(remap)
           statements.each do |statement|
             yielder << statement
           end
@@ -89,7 +89,7 @@ module BELRDF
             yielder << RDF::Statement.new(
               void_dataset_uri,
               RDF::DC.hasPart,
-              evidence_uri
+              nanopub_uri
             )
           end
         end

data/lib/bel/translator/plugins/rdf/writer.rb

@@ -27,22 +27,22 @@ module BELRDF
         @wrote_dataset    = false
       end
 
-      def <<(evidence)
+      def <<(nanopub)
         if !@wrote_dataset && @void_dataset_uri
-          void_dataset_triples = evidence.to_void_dataset(@void_dataset_uri)
+          void_dataset_triples = nanopub.to_void_dataset(@void_dataset_uri)
           if void_dataset_triples && void_dataset_triples.respond_to?(:each)
             void_dataset_triples.each do |void_triple|
               @writer.write_statement(void_triple)
             end
           end
         end
-        evidence_uri, statements = evidence.to_rdf
+        nanopub_uri, statements = nanopub.to_rdf
         statements.each do |statement|
           @writer.write_statement(statement)
         end
 
         if @void_dataset_uri
-          @writer.write_statement(RDF::Statement.new(@void_dataset_uri, RDF::DC.hasPart, evidence_uri))
+          @writer.write_statement(RDF::Statement.new(@void_dataset_uri, RDF::DC.hasPart, nanopub_uri))
         end
       end
 

data/lib/bel/translator/plugins/rdf2/belv2_0.rb

@@ -0,0 +1,416 @@
+require 'rdf'
+require 'rdf/turtle'
+require 'rdf/vocab'
+
+module BEL
+  module BELRDF
+
+    # Vocabulary constant for Nanopub instances (non-strict).
+    BELN   = RDF::Vocabulary.new('http://www.openbel.org/nanopub/')
+    BELR   = RDF::Vocabulary.new('http://www.openbel.org/bel/')
+    PUBMED = RDF::Vocabulary.new('http://bio2rdf.org/pubmed:')
+
+    class BELV2_0 < RDF::StrictVocabulary('http://www.openbel.org/vocabulary/')
+      RDFS = RDF::Vocab::RDFS
+      SKOS = RDF::Vocab::SKOS
+      XSD  = RDF::Vocab::XSD
+
+      # Concept classes
+      term :AnnotationConcept,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => SKOS.Concept
+      term :AnnotationConceptScheme,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => SKOS.ConceptScheme
+      term :NamespaceConcept,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => SKOS.Concept
+      term :NamespaceConceptScheme,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => SKOS.ConceptScheme
+      term :AbundanceConcept,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.NamespaceConcept
+      term :BiologicalProcessConcept,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.NamespaceConcept
+      term :ComplexConcept,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.AbundanceConcept
+      term :CompositeConcept,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.AbundanceConcept
+      term :GeneConcept,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.AbundanceConcept
+      term :LocationConcept,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.NamespaceConcept
+      term :RNAConcept,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.AbundanceConcept
+      term :MicroRNAConcept,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.RNAConcept
+      term :MolecularActivityConcept,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.NamespaceConcept
+      term :PathologyConcept,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.BiologicalProcessConcept
+      term :ProteinConcept,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.AbundanceConcept
+      term :ProteinModificationConcept,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.NamespaceConcept
+
+      # Nanopub classes
+      term :Abundance,
+        RDF.type           => RDFS.Class
+      term :Nanopub,
+        RDF.type           => RDFS.Class
+      term :Process,
+        RDF.type           => RDFS.Class
+      term :Relationship,
+        RDF.type           => RDFS.Class
+      term :Statement,
+        RDF.type           => RDFS.Class
+      term :Term,
+        RDF.type           => RDFS.Class
+
+      # BiologicalExpressionLanguage class
+      term :BiologicalExpressionLanguage,
+        RDF.type           => RDFS.Class
+
+      # Relationship categories
+      term :CausalRelationship,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Relationship
+      term :CorrelativeRelationship,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Relationship
+      term :DirectRelationship,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Relationship
+      term :GenomicRelationship,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Relationship
+      term :MembershipRelationship,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Relationship
+      term :NegativeRelationship,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Relationship
+      term :PositiveRelationship,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Relationship
+
+      # Relationship types
+      term :Analogous,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.GenomicRelationship
+      term :BiomarkerFor,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Relationship
+      term :Association,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.CorrelativeRelationship
+      term :CausesNoChange,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.CausalRelationship
+      term :Decreases,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => [
+          BELV2_0.CausalRelationship,
+          BELV2_0.NegativeRelationship
+        ]
+      term :DirectlyDecreases,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => [
+          BELV2_0.CausalRelationship,
+          BELV2_0.Decreases,
+          BELV2_0.DirectRelationship,
+          BELV2_0.NegativeRelationship
+        ]
+      term :Increases,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.CausalRelationship
+      term :DirectlyIncreases,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => [
+          BELV2_0.CausalRelationship,
+          BELV2_0.DirectRelationship,
+          BELV2_0.Increases,
+          BELV2_0.PositiveRelationship
+        ]
+      term :HasComponent,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.MembershipRelationship
+      term :HasMember,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.MembershipRelationship
+      term :IsA,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.MembershipRelationship
+      term :NegativeCorrelation,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => [
+          BELV2_0.CorrelativeRelationship,
+          BELV2_0.NegativeRelationship
+        ]
+      term :Orthologous,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.GenomicRelationship
+      term :PositiveCorrelation,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => [
+          BELV2_0.CorrelativeRelationship,
+          BELV2_0.PositiveRelationship
+        ]
+      term :PrognosticBiomarkerFor,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.BiomarkerFor
+      term :SubProcessOf,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.MembershipRelationship
+      term :RateLimitingStepOf,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => [
+          BELV2_0.CausalRelationship, BELV2_0.Increases, BELV2_0.SubProcessOf
+        ]
+      term :Regulates,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.CausalRelationship
+      term :TranscribedTo,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.GenomicRelationship
+      term :TranslatedTo,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.GenomicRelationship
+
+      # Process classes
+      term :BiologicalProcess,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Process
+      term :Transformation,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Process
+      term :Translocation,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Transformation
+      term :CellSecretion,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Translocation
+      term :CellSurfaceExpression,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Translocation
+      term :Degradation,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Transformation
+      term :Pathology,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.BiologicalProcess
+      term :Reaction,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Transformation
+
+      # Abundance classes
+      term :ComplexAbundance,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Abundance
+      term :CompositeAbundance,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Abundance
+      term :FusionAbundance,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Abundance
+      term :GeneAbundance,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Abundance
+      term :MicroRNAAbundance,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Abundance
+      term :ProteinAbundance,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Abundance
+      term :ModifiedProteinAbundance,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.ProteinAbundance
+      term :RNAAbundance,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Abundance
+
+      # Molecular activities e.g. act(p(HGNC:FOXO1), ma(tscript))
+      term :Activity,
+        RDF.type           => RDFS.Class,
+        RDFS.subClassOf    => BELV2_0.Process
+
+      # Protein modification
+      term :ProteinModification,
+        RDF.type           => RDFS.Class
+
+      # Molecular activity properties
+      property :hasActivityAbundance,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.Activity,
+        RDFS.range         => BELV2_0.Abundance
+      property :hasActivityType,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.Activity,
+        RDFS.range         => BELV2_0.MolecularActivityConcept
+
+      # Fusion properties
+      property :hasBeginAbundance,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.FusionAbundance,
+        RDFS.range         => BELV2_0.Abundance
+      property :hasBeginRange,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.FusionAbundance,
+        RDFS.range         => XSD.string
+      property :hasEndAbundance,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.FusionAbundance,
+        RDFS.range         => BELV2_0.Abundance
+      property :hasEndRange,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.FusionAbundance,
+        RDFS.range         => XSD.string
+
+      # Protein modification properties
+      property :hasModifiedProteinAbundance,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.ProteinAbundance,
+        RDFS.range         => BELV2_0.ModifiedProteinAbundance
+      property :hasProteinModification,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.ModifiedProteinAbundance,
+        RDFS.range         => BELV2_0.ProteinModification
+      property :hasProteinModificationType,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.ProteinModification,
+        RDFS.range         => BELV2_0.ProteinModificationConcept
+      property :hasAminoAcid,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.ProteinModification,
+        RDFS.range         => XSD.string
+      property :hasProteinResidue,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.ProteinModification,
+        RDFS.range         => XSD.integer
+
+      # Reaction properties
+      property :hasProduct,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.Reaction,
+        RDFS.range         => BELV2_0.Abundance
+      property :hasReactant,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.Reaction,
+        RDFS.range         => BELV2_0.Abundance
+
+
+      # Variant properties
+      property :hasVariant,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => [
+          BELV2_0.GeneAbundance,
+          BELV2_0.MicroRNAAbundance,
+          BELV2_0.ProteinAbundance,
+          BELV2_0.RNAAbundance
+        ],
+        RDFS.range         => XSD.string
+
+      # Cellular location properties
+      property :hasLocation,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => [
+          BELV2_0.ComplexAbundance,
+          BELV2_0.GeneAbundance,
+          BELV2_0.MicroRNAAbundance,
+          BELV2_0.ProteinAbundance,
+          BELV2_0.RNAAbundance
+        ],
+        RDFS.range         => BELV2_0.LocationConcept
+      property :hasFromLocation,
+        RDF.type           => RDF.Property,
+        RDFS.subPropertyOf => BELV2_0.hasLocation,
+        RDFS.domain        => BELV2_0.Translocation,
+        RDFS.range         => BELV2_0.LocationConcept
+      property :hasToLocation,
+        RDF.type           => RDF.Property,
+        RDFS.subPropertyOf => BELV2_0.hasLocation,
+        RDFS.domain        => BELV2_0.Translocation,
+        RDFS.range         => BELV2_0.LocationConcept
+
+      # Fragment properties
+      property :hasFragmentRange,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.ProteinAbundance,
+        RDFS.range         => XSD.string
+      property :hasFragmentDescriptor,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.ProteinAbundance,
+        RDFS.range         => XSD.string
+
+      # Term properties
+      property :hasChild,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.Term,
+        RDFS.range         => BELV2_0.Term
+      property :hasConcept,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.Term,
+        RDFS.range         => BELV2_0.NamespaceConcept
+
+      # Statement properties
+      property :hasSubject,
+        RDF.type           => RDF.Property,
+        RDFS.subPropertyOf => BELV2_0.hasChild,
+        RDFS.domain        => BELV2_0.Statement,
+        RDFS.range         => BELV2_0.Term
+      property :hasRelationship,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.Statement,
+        RDFS.range         => BELV2_0.Relationship
+      property :hasObject,
+        RDF.type           => RDF.Property,
+        RDFS.subPropertyOf => BELV2_0.hasChild,
+        RDFS.domain        => BELV2_0.Statement,
+        RDFS.range         => BELV2_0.Term
+      property :hasNanopub,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.Statement,
+        RDFS.range         => BELV2_0.Nanopub
+
+      # Nanopub properties
+      property :hasAnnotation,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.Nanopub,
+        RDFS.range         => BELV2_0.AnnotationConcept
+      property :hasCitation,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.Nanopub,
+        RDFS.range         => RDFS.Resource
+      property :hasSupport,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.Nanopub,
+        RDFS.range         => XSD.string
+      property :hasStatement,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.Nanopub,
+        RDFS.range         => BELV2_0.Statement
+      property :hasBiologicalExpressionLanguage,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.Nanopub,
+        RDFS.range         => BELV2_0.BiologicalExpressionLanguage
+
+      # BiologicalExpressionLanguage properties
+      property :hasVersion,
+        RDF.type           => RDF.Property,
+        RDFS.domain        => BELV2_0.BiologicalExpressionLanguage,
+        RDFS.range         => XSD.string
+    end
+  end
+end