@prefix : . @prefix dc: . @prefix owl: . @prefix rdf: . @prefix rsa: . @prefix xml: . @prefix xsd: . @prefix rdfs: . @base . rdf:type owl:Ontology ; dc:created "2012-10-08"^^xsd:date ; dc:modified "2014-1-31"^^xsd:dateTime ; dc:contributor "Andrew P. Gibson"^^xsd:string , "Jeroen F.J. Laros"^^xsd:string ; dc:creator "Zuotian Tatum"^^xsd:string ; owl:versionInfo "0.6" . ################################################################# # # Object Properties # ################################################################# ### http://rdf.biosemantics.org/ontologies/rsa#hasOrientation rsa:hasOrientation rdf:type owl:FunctionalProperty , owl:ObjectProperty ; rdfs:comment "a transcript annotation may have forward orientation on the reference sequence of a chromosome."@en ; rdfs:domain rsa:AnnotationLocation ; rdfs:range rsa:Orientation . ### http://rdf.biosemantics.org/ontologies/rsa#isAnnotatedAt rsa:isAnnotatedAt rdf:type owl:ObjectProperty ; rdfs:comment "an annotation is annotated at a location on a reference sequence."@en ; rdfs:range rsa:AnnotationLocation ; rdfs:domain rsa:SequenceAnnotation . ### http://rdf.biosemantics.org/ontologies/rsa#mapsTo rsa:mapsTo rdf:type owl:ObjectProperty ; rdfs:comment "how an annotation can be places and orientated on a reference sequence."@en ; rdfs:range rsa:AnnotationLocation ; rdfs:domain rsa:SequenceAnnotation . ### http://rdf.biosemantics.org/ontologies/rsa#regionOf rsa:regionOf rdf:type owl:ObjectProperty ; rdfs:domain rsa:AnnotationLocation ; rdfs:range rsa:ReferenceSequence ; rdfs:subPropertyOf rsa:mapsTo . ################################################################# # # Data properties # ################################################################# ### http://rdf.biosemantics.org/ontologies/rsa#after rsa:after rdf:type owl:DatatypeProperty ; rdfs:domain rsa:Junction . ### http://rdf.biosemantics.org/ontologies/rsa#at rsa:at rdf:type owl:DatatypeProperty ; rdfs:domain rsa:Point . ### http://rdf.biosemantics.org/ontologies/rsa#before rsa:before rdf:type owl:DatatypeProperty ; rdfs:domain rsa:Junction . ### http://rdf.biosemantics.org/ontologies/rsa#end rsa:end rdf:type owl:DatatypeProperty ; rdfs:domain rsa:Region . ### http://rdf.biosemantics.org/ontologies/rsa#genBankID rsa:genBankID rdf:type owl:DatatypeProperty ; rdfs:domain rsa:ReferenceSequence . ### http://rdf.biosemantics.org/ontologies/rsa#geneBankAssemblyID rsa:geneBankAssemblyID rdf:type owl:DatatypeProperty . ### http://rdf.biosemantics.org/ontologies/rsa#refSeqID rsa:refSeqID rdf:type owl:DatatypeProperty ; rdfs:domain rsa:ReferenceSequence . ### http://rdf.biosemantics.org/ontologies/rsa#start rsa:start rdf:type owl:DatatypeProperty ; rdfs:domain rsa:Region . ################################################################# # # Classes # ################################################################# ### http://rdf.biosemantics.org/ontologies/rsa#AnnotationLocation rsa:AnnotationLocation rdf:type owl:Class ; rdfs:label "annotation location"^^xsd:string ; rdfs:comment "A location is considered as an instance separate from the annotation. A single annotation can be associated with multiple locations and a single location can be associated with multiple annotations. "@en , "Similar to annotation constraint in OA. Not a BFO:spacial_region."@en , "The location of an annotated sequence feature on a reference sequence."@en . ### http://rdf.biosemantics.org/ontologies/rsa#FeatureAnnotation rsa:FeatureAnnotation rdf:type owl:Class ; rdfs:subClassOf rsa:SequenceAnnotation ; rdfs:comment "feature annotation"^^xsd:string , "Place holder." . ### http://rdf.biosemantics.org/ontologies/rsa#GenomeAssembly rsa:GenomeAssembly rdf:type owl:Class ; rdfs:label "reference assembly"^^xsd:string ; rdfs:comment "An information entity encapsulating a set of RSA:ReferenceSequences that are often used together to represent the total sequence content of an organism. "@en , "Its version number (in some cases, the timestamp) is crucial for data integration."@en , "RSA:ReferenceSequence is RO:proper_part_of RSA:ReferenceAssembly. "@en . ### http://rdf.biosemantics.org/ontologies/rsa#Junction rsa:Junction rdf:type owl:Class ; rdfs:subClassOf rsa:AnnotationLocation . ### http://rdf.biosemantics.org/ontologies/rsa#Orientation rsa:Orientation rdf:type owl:Class ; rdfs:label "orientation"^^xsd:string ; rdfs:subClassOf [ rdf:type owl:Class ; owl:oneOf ( rsa:bidirectional rsa:reverse rsa:none rsa:forward ) ] ; rdfs:comment "example: gene DMD has reverse orientation on the reference sequence representing chromosome X."@en , "model the stranded-ness in double strand sequences and how annotations can be interpreted on single strand sequences."@en . ### http://rdf.biosemantics.org/ontologies/rsa#Point rsa:Point rdf:type owl:Class ; rdfs:subClassOf rsa:AnnotationLocation . ### http://rdf.biosemantics.org/ontologies/rsa#ReferenceSequence rsa:ReferenceSequence rdf:type owl:Class ; rdfs:label "reference sequence"^^xsd:string ; rdfs:comment "Both transcript sequences and chromosome sequences can be used as reference sequences, so instances of RSA:ReferenceSequence can be ro:proper_part_of another instance. This part of relationship is important for data integration scenarios, and this part of relationship works only if RSA:SequenceAnnotation is defined by the sequence content, as the sequence content of a transcript can be part of the sequence content of a chromosome, but not by the physical bearer of the sequence (a file)."@en , "It can represent sequential information captured by a biological molecule, but may represent a (possibly empty) set of molecules."@en , "Syntactic sequences that has a role as reference of an annotation. Instances of this class are sequence representations such as a FASTA file."@en . ### http://rdf.biosemantics.org/ontologies/rsa#Region rsa:Region rdf:type owl:Class ; rdfs:subClassOf rsa:AnnotationLocation . ### http://rdf.biosemantics.org/ontologies/rsa#SequenceAnnotation rsa:SequenceAnnotation rdf:type owl:Class ; rdfs:label "sequence annotation"^^xsd:string ; rdfs:comment "a narrower concept than SO:sequence_feature. Only represent the abstract sequences that represent molecular sequences."@en . ### http://rdf.biosemantics.org/ontologies/rsa#VariationAnnotation rsa:VariationAnnotation rdf:type owl:Class ; rdfs:label "variation annotation"^^xsd:string ; rdfs:subClassOf rsa:SequenceAnnotation ; rdfs:comment "Place holder." . ################################################################# # # Individuals # ################################################################# ### http://rdf.biosemantics.org/ontologies/rsa#bidirectional rsa:bidirectional rdf:type rsa:Orientation , owl:NamedIndividual . ### http://rdf.biosemantics.org/ontologies/rsa#forward rsa:forward rdf:type rsa:Orientation , owl:NamedIndividual ; rdfs:label "forward"^^rdfs:Literal . ### http://rdf.biosemantics.org/ontologies/rsa#none rsa:none rdf:type rsa:Orientation , owl:NamedIndividual . ### http://rdf.biosemantics.org/ontologies/rsa#reverse rsa:reverse rdf:type rsa:Orientation , owl:NamedIndividual ; rdfs:label "reverse"^^rdfs:Literal . ### http://rdf.biosemantics.org/ontologies/rsa#test rsa:test rdf:type owl:NamedIndividual . ### Generated by the OWL API (version 3.4.2) http://owlapi.sourceforge.net