@prefix dct: .
@prefix obo: .
@prefix owl: .
@prefix rdf: .
@prefix sio: .
@prefix xml: .
@prefix xsd: .
@prefix orth: .
@prefix rdfs: .
@base .
[ rdf:type owl:Ontology ;
owl:versionInfo """This ontology is a release candidate of a second version of the orthology ontology previously published in 2015 and available on http://purl.bioontology.org/ontology/ORTH .
@authors H. Chiba, J.T. Fernandez-Breis and T.M. de Farias"""@en
] .
#################################################################
# Annotation properties
#################################################################
### http://purl.org/net/orth#inDatabase
orth:inDatabase rdf:type owl:AnnotationProperty ;
rdfs:comment "A property to define the database an orthology dataset belongs to."@en ;
rdfs:label "in database"@en ;
rdfs:domain orth:OrthologyDataset .
#################################################################
# Object Properties
#################################################################
### http://purl.obolibrary.org/obo/CDAO_0000178
obo:CDAO_0000178 rdf:type owl:ObjectProperty .
### http://purl.obolibrary.org/obo/CDAO_0000194
obo:CDAO_0000194 rdf:type owl:ObjectProperty .
### http://purl.obolibrary.org/obo/RO_0001018
obo:RO_0001018 rdf:type owl:ObjectProperty ;
rdfs:label "contained in"@en .
### http://purl.obolibrary.org/obo/RO_0002162
obo:RO_0002162 rdf:type owl:ObjectProperty ;
rdfs:label "in taxon"@en .
### http://purl.obolibrary.org/obo/RO_0002350
obo:RO_0002350 rdf:type owl:ObjectProperty ;
rdfs:label "member of"@en .
### http://purl.org/net/orth#hasCluster
orth:hasCluster rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf obo:CDAO_0000178 ;
owl:inverseOf orth:inDataset ;
rdfs:domain orth:OrthologyDataset ;
rdfs:range orth:HomologsCluster ;
rdfs:comment "Inverse property of inDataset. It permits to navigate to the clusters included in a particular dataset."@en ;
rdfs:label "Has cluster"@en .
### http://purl.org/net/orth#hasHomolog
orth:hasHomolog rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf obo:CDAO_0000178 ;
rdf:type owl:SymmetricProperty ;
rdfs:domain orth:SequenceUnit ;
rdfs:range orth:SequenceUnit .
### http://purl.org/net/orth#hasHomologousMember
orth:hasHomologousMember rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf sio:SIO_000028 ;
owl:inverseOf orth:isHomologousMember ;
rdfs:comment "Property that permits to define the membership of a cluster of homologs or a sequence unit to a clusters of homologs."@en ;
rdfs:label "has homologous member"@en .
### http://purl.org/net/orth#hasOrtholog
orth:hasOrtholog rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf orth:hasHomolog ;
rdf:type owl:SymmetricProperty ;
rdfs:comment "Orthologous pairwise relation between genes/proteins. For example, A Gene(A) hasOrtholog Gene(B). This property can be materialized or inferred by applying a logical rule or a sub-query."@en .
### http://purl.org/net/orth#hasParalog
orth:hasParalog rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf orth:hasHomolog ;
rdf:type owl:SymmetricProperty .
### http://purl.org/net/orth#hasTaxonomicRange
orth:hasTaxonomicRange rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf obo:CDAO_0000178 ;
rdfs:domain orth:HomologsCluster ;
rdfs:range orth:TaxonomicRange ;
rdfs:comment "Property that associates a cluster of homologs with the taxonomic range at which it has been calculated"@en ;
rdfs:label "Has taxonomic range"@en .
### http://purl.org/net/orth#hasXenolog
orth:hasXenolog rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf orth:hasHomolog ;
rdf:type owl:SymmetricProperty .
### http://purl.org/net/orth#inDataset
orth:inDataset rdf:type owl:ObjectProperty ;
rdfs:domain orth:GeneTreeNode ;
rdfs:range orth:OrthologyDataset ;
rdfs:comment "Property that provides the dataset associated with a gene tree node"@en .
### http://purl.org/net/orth#isHomologousMember
orth:isHomologousMember rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf obo:RO_0002350 ;
rdfs:comment "Inverse of has homologous member. This property permits to find the cluster in which a cluster or sequence unit is included."@en ;
rdfs:label "is homologous member"@en .
### http://semanticscience.org/resource/SIO_000028
sio:SIO_000028 rdf:type owl:ObjectProperty .
### http://semanticscience.org/resource/SIO_010078
sio:SIO_010078 rdf:type owl:ObjectProperty .
#################################################################
# Data properties
#################################################################
### http://purl.org/dc/terms/identifier
dct:identifier rdf:type owl:DatatypeProperty ;
rdfs:range xsd:string ;
rdfs:label "identifier"@en .
### http://purl.org/net/orth#taxRange
orth:taxRange rdf:type owl:DatatypeProperty ;
rdfs:domain orth:TaxonomicRange ;
rdfs:range xsd:string ;
rdfs:comment "Property that stores the name of the taxonomic range at which a given cluster of homologs has been calculated"@en ;
rdfs:label "tax range"@en .
### http://purl.org/net/orth#taxRangeId
orth:taxRangeId rdf:type owl:DatatypeProperty ;
rdfs:range xsd:integer ;
rdfs:comment "This property links a cluster of homologs with its taxonomic range."@en ;
rdfs:label "tax range id"@en .
### http://purl.org/pav#version
rdf:type owl:DatatypeProperty ;
rdfs:label "version"@en .
#################################################################
# Classes
#################################################################
### http://purl.obolibrary.org/obo/CDAO_0000012
obo:CDAO_0000012 rdf:type owl:Class ;
rdfs:comment "Tree with a root node, which is the common ancestor to all the nodes in the tree"@en .
### http://purl.obolibrary.org/obo/CDAO_0000064
obo:CDAO_0000064 rdf:type owl:Class ;
rdfs:comment "Evolutionary event"@en .
### http://purl.obolibrary.org/obo/CDAO_0000077
obo:CDAO_0000077 rdf:type owl:Class ;
rdfs:comment "Evolutionary event that consists on the duplication of a gene"@en .
### http://purl.obolibrary.org/obo/CDAO_0000121
obo:CDAO_0000121 rdf:type owl:Class ;
rdfs:comment "Evolutionary event related with the evolution of a gene in different species"@en .
### http://purl.obolibrary.org/obo/CDAO_0000138
obo:CDAO_0000138 rdf:type owl:Class .
### http://purl.obolibrary.org/obo/CDAO_0000140
obo:CDAO_0000140 rdf:type owl:Class ;
rdfs:comment "Basic unit of graphs and trees"@en .
### http://purl.obolibrary.org/obo/NCBITaxon_1
obo:NCBITaxon_1 rdf:type owl:Class ;
rdfs:comment "Species"@en .
### http://purl.obolibrary.org/obo/SO_0000104
obo:SO_0000104 rdf:type owl:Class ;
owl:equivalentClass orth:Protein .
### http://purl.obolibrary.org/obo/SO_0000704
obo:SO_0000704 rdf:type owl:Class ;
owl:equivalentClass orth:Gene .
### http://purl.obolibrary.org/obo/SO_0001411
obo:SO_0001411 rdf:type owl:Class .
### http://purl.obolibrary.org/obo/SO_0005855
obo:SO_0005855 rdf:type owl:Class .
### http://purl.org/net/orth#Gene
orth:Gene rdf:type owl:Class ;
rdfs:subClassOf orth:SequenceUnit ,
[ rdf:type owl:Restriction ;
owl:onProperty obo:RO_0001018 ;
owl:someValuesFrom sio:SIO_000750
] ,
[ rdf:type owl:Restriction ;
owl:onProperty obo:RO_0002162 ;
owl:someValuesFrom obo:NCBITaxon_1
] .
### http://purl.org/net/orth#GeneTreeNode
orth:GeneTreeNode rdf:type owl:Class ;
rdfs:subClassOf obo:CDAO_0000140 ;
rdfs:comment "A node of a tree whose leaf nodes are sequence units and whose internal nodes are clusters of homologs"@en ;
rdfs:label "Gene tree node"@en .
### http://purl.org/net/orth#HierarchicalClusteringTree
orth:HierarchicalClusteringTree rdf:type owl:Class ;
rdfs:subClassOf obo:CDAO_0000012 ;
rdfs:comment "A tree whose content is the result of the application of hierarchical clustering to a dataset"@en ;
rdfs:label "Hierarchical clustering tree"@en .
### http://purl.org/net/orth#HierarchicalGeneTree
orth:HierarchicalGeneTree rdf:type owl:Class ;
rdfs:subClassOf orth:HierarchicalClusteringTree ,
[ rdf:type owl:Restriction ;
owl:onProperty obo:CDAO_0000178 ;
owl:someValuesFrom orth:Gene
] ,
[ rdf:type owl:Restriction ;
owl:onProperty obo:CDAO_0000178 ;
owl:allValuesFrom orth:GeneTreeNode
] ;
rdfs:comment "A tree whose leaf nodes correspond to genes"@en ;
rdfs:label "Hierarchical gene tree "@en .
### http://purl.org/net/orth#HomologsCluster
orth:HomologsCluster rdf:type owl:Class ;
rdfs:subClassOf obo:SO_0005855 ,
orth:GeneTreeNode ,
[ rdf:type owl:Restriction ;
owl:onProperty orth:inDataset ;
owl:someValuesFrom orth:OrthologyDataset
] ,
[ rdf:type owl:Restriction ;
owl:onProperty obo:CDAO_0000178 ;
owl:allValuesFrom obo:CDAO_0000064
] ,
[ rdf:type owl:Restriction ;
owl:onProperty orth:hasHomologousMember ;
owl:allValuesFrom orth:GeneTreeNode
] ,
[ rdf:type owl:Restriction ;
owl:onProperty orth:hasTaxonomicRange ;
owl:allValuesFrom orth:TaxonomicRange
] ;
rdfs:comment "Set of homologous sequences"@en ;
rdfs:label "Cluster of homologs"@en .
### http://purl.org/net/orth#OrthologsCluster
orth:OrthologsCluster rdf:type owl:Class ;
rdfs:subClassOf orth:HomologsCluster ,
[ rdf:type owl:Restriction ;
owl:onProperty obo:CDAO_0000178 ;
owl:allValuesFrom obo:CDAO_0000121
] ;
rdfs:comment """Set of homologous sequences derived from a speciation event.
"""@en ;
rdfs:label "Cluster of orthologs"@en ,
"homologous cluster"@en .
### http://purl.org/net/orth#OrthologyDataset
orth:OrthologyDataset rdf:type owl:Class ;
rdfs:subClassOf [ rdf:type owl:Restriction ;
owl:onProperty ;
owl:someValuesFrom xsd:string
] ;
rdfs:comment "A resource that provides information about orthology" ;
rdfs:label "Orthology dataset"@en .
### http://purl.org/net/orth#ParalogsCluster
orth:ParalogsCluster rdf:type owl:Class ;
rdfs:subClassOf orth:HomologsCluster ,
[ rdf:type owl:Restriction ;
owl:onProperty obo:CDAO_0000178 ;
owl:allValuesFrom obo:CDAO_0000077
] ;
rdfs:comment "Set of homologous sequences derived from a duplication event"@en ;
rdfs:label "Cluster of paralogs"@en .
### http://purl.org/net/orth#Protein
orth:Protein rdf:type owl:Class ;
rdfs:subClassOf orth:SequenceUnit ,
[ rdf:type owl:Restriction ;
owl:onProperty obo:RO_0001018 ;
owl:someValuesFrom sio:SIO_000750
] ,
[ rdf:type owl:Restriction ;
owl:onProperty obo:RO_0002162 ;
owl:someValuesFrom obo:NCBITaxon_1
] .
### http://purl.org/net/orth#SequenceUnit
orth:SequenceUnit rdf:type owl:Class ;
rdfs:subClassOf obo:CDAO_0000138 ,
obo:SO_0001411 ,
orth:GeneTreeNode ;
rdfs:comment "protein or DNA sequence as a unit of comparison"@en ;
rdfs:label "Sequence unit"@en .
### http://purl.org/net/orth#Subgene
orth:Subgene rdf:type owl:Class ;
rdfs:subClassOf orth:SequenceUnit ,
[ rdf:type owl:Restriction ;
owl:onProperty obo:CDAO_0000194 ;
owl:someValuesFrom orth:Gene
] ;
rdfs:comment "A region of the sequence of the gene"@en ;
rdfs:label "Subgene"@en .
### http://purl.org/net/orth#TaxonomicRange
orth:TaxonomicRange rdf:type owl:Class ;
rdfs:comment "The taxonomic range represents the taxon at which a group of sequences are considered members of the same cluster of orthologs/paralogs"@en ;
rdfs:label "Taxonomic range"@en .
### http://semanticscience.org/resource/SIO_000750
sio:SIO_000750 rdf:type owl:Class .
### http://semanticscience.org/resource/SIO_010100
sio:SIO_010100 rdf:type owl:Class .
### Generated by the OWL API (version 4.2.8.20170104-2310) https://github.com/owlcs/owlapi