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oo.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.org/net/orth#"
xml:base="http://purl.org/net/orth"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:orthology="http://purl.org/net/orth#"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:so-xp="http://purl.obolibrary.org/obo/so-xp.obo#"
xmlns:ncbi="http://miuras.inf.um.es/ontologies/swit/ncbi.owl#"
xmlns:cito="http://purl.org/spar/cito/"
xmlns:biositemap="http://bioontology.org/ontologies/biositemap.owl#"
xmlns:dct="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:sio="http://semanticscience.org/resource/"
xmlns:vann="http://purl.org/vocab/vann/"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#">
<owl:Ontology rdf:about="http://purl.org/net/orth">
<owl:imports rdf:resource="http://miuras.inf.um.es/ontologies/swit/ncbi.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/cdao.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<owl:imports rdf:resource="http://semanticscience.org/ontology/sio.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://www.w3.org/2000/01/rdf-schema#description -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#description"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://bioontology.org/ontologies/biositemap.owl#version_information -->
<owl:ObjectProperty rdf:about="http://bioontology.org/ontologies/biositemap.owl#version_information">
<rdfs:label xml:lang="en">version information</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/CDAO_0000178 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/CDAO_0000178"/>
<!-- http://purl.obolibrary.org/obo/CDAO_0000194 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/CDAO_0000194"/>
<!-- http://purl.obolibrary.org/obo/RO_0001018 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001018">
<rdfs:label xml:lang="en">contained in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002162 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002162">
<rdfs:label xml:lang="en">in taxon</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002350 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002350">
<rdfs:label xml:lang="en">member of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/net/orth#hasCluster -->
<owl:ObjectProperty rdf:about="http://purl.org/net/orth#hasCluster">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000178"/>
<owl:inverseOf rdf:resource="http://rdfs.org/ns/void#inDataset"/>
<rdfs:range rdf:resource="http://purl.org/net/orth#GeneTreeNode"/>
<rdfs:description xml:lang="en">Inverse property of inDataset. It permits to navigate to the clusters included in a particular dataset.</rdfs:description>
<rdfs:label xml:lang="en">Has cluster</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/net/orth#hasHomologous -->
<owl:ObjectProperty rdf:about="http://purl.org/net/orth#hasHomologous">
<rdfs:subPropertyOf rdf:resource="http://semanticscience.org/resource/SIO_000028"/>
<owl:inverseOf rdf:resource="http://purl.org/net/orth#isHomologMember"/>
<rdfs:description xml:lang="en">Property that permits to define the membership of a cluster of homologs or a sequence unit to a clusters of homologs </rdfs:description>
<rdfs:label xml:lang="en">Has homologous</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/net/orth#hasSource -->
<owl:ObjectProperty rdf:about="http://purl.org/net/orth#hasSource">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000178"/>
<rdfs:domain rdf:resource="http://purl.org/net/orth#OrthologyDataset"/>
<rdfs:range rdf:resource="http://www.w3.org/2000/01/rdf-schema#Resource"/>
<rdfs:description xml:lang="en">It permits to link a cluster with its data source</rdfs:description>
<rdfs:label xml:lang="en">Has source</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/net/orth#hasTaxonomicRange -->
<owl:ObjectProperty rdf:about="http://purl.org/net/orth#hasTaxonomicRange">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000178"/>
<rdfs:domain rdf:resource="http://purl.org/net/orth#HomologsCluster"/>
<rdfs:range rdf:resource="http://purl.org/net/orth#TaxonomicRange"/>
<rdfs:description xml:lang="en">Property that associates a cluster of homologs with the taxonomic range at which it has been calculated</rdfs:description>
<rdfs:label xml:lang="en">Has taxonomic range</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/net/orth#isHomologMember -->
<owl:ObjectProperty rdf:about="http://purl.org/net/orth#isHomologMember">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002350"/>
<rdfs:description xml:lang="en">Inverse of has homologous. This property permits to find the cluster in which a cluster or sequence unit is included.</rdfs:description>
<rdfs:label xml:lang="en">Is homologous member</rdfs:label>
</owl:ObjectProperty>
<!-- http://rdfs.org/ns/void#inDataset -->
<owl:ObjectProperty rdf:about="http://rdfs.org/ns/void#inDataset">
<rdfs:domain rdf:resource="http://purl.org/net/orth#GeneTreeNode"/>
<rdfs:range rdf:resource="http://purl.org/net/orth#OrthologyDataset"/>
<rdfs:description xml:lang="en">Property that provides the dataset associated with a gene tree node</rdfs:description>
<rdfs:label xml:lang="en">In dataset</rdfs:label>
</owl:ObjectProperty>
<!-- http://semanticscience.org/resource/SIO_000028 -->
<owl:ObjectProperty rdf:about="http://semanticscience.org/resource/SIO_000028"/>
<!-- http://semanticscience.org/resource/SIO_010078 -->
<owl:ObjectProperty rdf:about="http://semanticscience.org/resource/SIO_010078"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Data properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://bioontology.org/ontologies/biositemap.owl#description -->
<owl:DatatypeProperty rdf:about="http://bioontology.org/ontologies/biositemap.owl#description">
<rdfs:label xml:lang="en">description</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.org/dc/terms/identifier -->
<owl:DatatypeProperty rdf:about="http://purl.org/dc/terms/identifier">
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
<rdfs:label xml:lang="en">identifier</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.org/net/orth#taxRange -->
<owl:DatatypeProperty rdf:about="http://purl.org/net/orth#taxRange">
<rdfs:domain rdf:resource="http://purl.org/net/orth#TaxonomicRange"/>
<rdfs:description xml:lang="en">Property that stores the name of the taxonomic range at which a given cluster of homologs has been calculated</rdfs:description>
<rdfs:label xml:lang="en">tax range</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.org/net/orth#taxRangeId -->
<owl:DatatypeProperty rdf:about="http://purl.org/net/orth#taxRangeId">
<rdfs:description xml:lang="en">This property links a cluster of homologs with its taxonomic range.</rdfs:description>
<rdfs:label xml:lang="en">tax range id</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.org/pav#version -->
<owl:DatatypeProperty rdf:about="http://purl.org/pav#version">
<rdfs:label xml:lang="en">version</rdfs:label>
</owl:DatatypeProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://identifiers.org/taxonomy -->
<owl:Class rdf:about="http://identifiers.org/taxonomy">
<rdfs:label xml:lang="en">Taxon</rdfs:label>
</owl:Class>
<!-- http://miuras.inf.um.es/ontologies/swit/ncbi.owl#NCBI_1 -->
<rdf:Description rdf:about="http://miuras.inf.um.es/ontologies/swit/ncbi.owl#NCBI_1">
<rdfs:description xml:lang="en">Species</rdfs:description>
</rdf:Description>
<!-- http://purl.obolibrary.org/obo/CDAO_0000012 -->
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CDAO_0000012">
<rdfs:description xml:lang="en">Tree with a root node, which is the common ancestor to all the nodes in the tree</rdfs:description>
</rdf:Description>
<!-- http://purl.obolibrary.org/obo/CDAO_0000064 -->
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CDAO_0000064">
<rdfs:description xml:lang="en">Evolutionary event</rdfs:description>
</rdf:Description>
<!-- http://purl.obolibrary.org/obo/CDAO_0000077 -->
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CDAO_0000077">
<rdfs:description xml:lang="en">Evolutionary event that consists on the duplication of a gene</rdfs:description>
</rdf:Description>
<!-- http://purl.obolibrary.org/obo/CDAO_0000121 -->
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CDAO_0000121">
<rdfs:description xml:lang="en">Evolutionary event related with the evolution of a gene in different species</rdfs:description>
</rdf:Description>
<!-- http://purl.obolibrary.org/obo/CDAO_0000138 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CDAO_0000138"/>
<!-- http://purl.obolibrary.org/obo/CDAO_0000140 -->
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CDAO_0000140">
<rdfs:description xml:lang="en">Basic unit of graphs and trees</rdfs:description>
</rdf:Description>
<!-- http://purl.obolibrary.org/obo/SO_0000104 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000104">
<owl:equivalentClass rdf:resource="http://purl.org/net/orth#Protein"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000704 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000704">
<owl:equivalentClass rdf:resource="http://purl.org/net/orth#Gene"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001411 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001411"/>
<!-- http://purl.org/net/orth#Gene -->
<owl:Class rdf:about="http://purl.org/net/orth#Gene">
<rdfs:subClassOf rdf:resource="http://purl.org/net/orth#SequenceUnit"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:someValuesFrom rdf:resource="http://miuras.inf.um.es/ontologies/swit/ncbi.owl#NCBI_1"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>
<!-- http://purl.org/net/orth#GeneTreeNode -->
<owl:Class rdf:about="http://purl.org/net/orth#GeneTreeNode">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000140"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.org/dc/terms/identifier"/>
<owl:someValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:description xml:lang="en">A node of a tree whose leaf nodes are sequence units and whose internal nodes are clusters of homologs</rdfs:description>
<rdfs:label xml:lang="en">Gene tree node</rdfs:label>
</owl:Class>
<!-- http://purl.org/net/orth#HierarchicalClusteringTree -->
<owl:Class rdf:about="http://purl.org/net/orth#HierarchicalClusteringTree">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000012"/>
<rdfs:description xml:lang="en">A tree whose content is the result of the application of hierarchical clustering to a dataset</rdfs:description>
<rdfs:label xml:lang="en">Hierarchical clustering tree</rdfs:label>
</owl:Class>
<!-- http://purl.org/net/orth#HierarchicalGeneTree -->
<owl:Class rdf:about="http://purl.org/net/orth#HierarchicalGeneTree">
<rdfs:subClassOf rdf:resource="http://purl.org/net/orth#HierarchicalClusteringTree"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000178"/>
<owl:someValuesFrom rdf:resource="http://purl.org/net/orth#Gene"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000178"/>
<owl:allValuesFrom rdf:resource="http://purl.org/net/orth#GeneTreeNode"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:description xml:lang="en">A tree whose leaf nodes correspond to genes</rdfs:description>
<rdfs:label xml:lang="en">Hierarchical gene tree </rdfs:label>
</owl:Class>
<!-- http://purl.org/net/orth#HomologsCluster -->
<owl:Class rdf:about="http://purl.org/net/orth#HomologsCluster">
<rdfs:subClassOf rdf:resource="http://purl.org/net/orth#GeneTreeNode"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://rdfs.org/ns/void#inDataset"/>
<owl:someValuesFrom rdf:resource="http://purl.org/net/orth#OrthologyDataset"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000178"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000064"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.org/net/orth#hasHomologous"/>
<owl:allValuesFrom rdf:resource="http://purl.org/net/orth#GeneTreeNode"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.org/net/orth#hasTaxonomicRange"/>
<owl:allValuesFrom rdf:resource="http://purl.org/net/orth#TaxonomicRange"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:description xml:lang="en">Set of homologous sequences</rdfs:description>
<rdfs:label xml:lang="en">Cluster of homologs</rdfs:label>
</owl:Class>
<!-- http://purl.org/net/orth#OrthologsCluster -->
<owl:Class rdf:about="http://purl.org/net/orth#OrthologsCluster">
<rdfs:subClassOf rdf:resource="http://purl.org/net/orth#HomologsCluster"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000178"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000121"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:description xml:lang="en">Set of homologous sequences derived from a speciation event.
</rdfs:description>
<rdfs:label xml:lang="en">Cluster of orthologs</rdfs:label>
</owl:Class>
<!-- http://purl.org/net/orth#OrthologyDataset -->
<owl:Class rdf:about="http://purl.org/net/orth#OrthologyDataset">
<rdfs:subClassOf rdf:resource="http://rdfs.org/ns/void#Dataset"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.org/net/orth#hasSource"/>
<owl:someValuesFrom rdf:resource="http://www.w3.org/2000/01/rdf-schema#Resource"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.org/pav#version"/>
<owl:someValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:description>A resource that provides information about orthology</rdfs:description>
<rdfs:label xml:lang="en">Orthology dataset</rdfs:label>
</owl:Class>
<!-- http://purl.org/net/orth#ParalogsCluster -->
<owl:Class rdf:about="http://purl.org/net/orth#ParalogsCluster">
<rdfs:subClassOf rdf:resource="http://purl.org/net/orth#HomologsCluster"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000178"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000077"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:description xml:lang="en">Set of homologous sequences derived from a duplication event</rdfs:description>
<rdfs:label xml:lang="en">Cluster of paralogs</rdfs:label>
</owl:Class>
<!-- http://purl.org/net/orth#Protein -->
<owl:Class rdf:about="http://purl.org/net/orth#Protein">
<rdfs:subClassOf rdf:resource="http://purl.org/net/orth#SequenceUnit"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0001018"/>
<owl:someValuesFrom rdf:resource="http://semanticscience.org/resource/SIO_000750"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>
<!-- http://purl.org/net/orth#SequenceUnit -->
<owl:Class rdf:about="http://purl.org/net/orth#SequenceUnit">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000138"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001411"/>
<rdfs:subClassOf rdf:resource="http://purl.org/net/orth#GeneTreeNode"/>
<rdfs:description xml:lang="en">protein or DNA sequence as a unit of comparison</rdfs:description>
<rdfs:label xml:lang="en">Sequence unit</rdfs:label>
</owl:Class>
<!-- http://purl.org/net/orth#Subgene -->
<owl:Class rdf:about="http://purl.org/net/orth#Subgene">
<rdfs:subClassOf rdf:resource="http://purl.org/net/orth#SequenceUnit"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000194"/>
<owl:someValuesFrom rdf:resource="http://purl.org/net/orth#Gene"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:description xml:lang="en">A region of the sequence of the gene</rdfs:description>
<rdfs:label xml:lang="en">Subgene</rdfs:label>
</owl:Class>
<!-- http://purl.org/net/orth#TaxonomicRange -->
<owl:Class rdf:about="http://purl.org/net/orth#TaxonomicRange">
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.org/net/orth#taxRange"/>
<owl:allValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.org/net/orth#taxRangeId"/>
<owl:allValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:description xml:lang="en">The taxonomic range represents the taxon at which a group of sequences are considered members of the same cluster of orthologs/paralogs</rdfs:description>
<rdfs:label xml:lang="en">Taxonomic range</rdfs:label>
</owl:Class>
<!-- http://rdfs.org/ns/void#Dataset -->
<owl:Class rdf:about="http://rdfs.org/ns/void#Dataset">
<rdfs:description xml:lang="en">Collection of data</rdfs:description>
<rdfs:label xml:lang="en">Dataset</rdfs:label>
</owl:Class>
<!-- http://semanticscience.org/resource/SIO_000750 -->
<owl:Class rdf:about="http://semanticscience.org/resource/SIO_000750"/>
<!-- http://semanticscience.org/resource/SIO_010100 -->
<owl:Class rdf:about="http://semanticscience.org/resource/SIO_010100"/>
<!-- http://www.w3.org/2000/01/rdf-schema#Resource -->
<owl:Class rdf:about="http://www.w3.org/2000/01/rdf-schema#Resource">
<rdfs:description xml:lang="en">The source of orthology information (e.g., database)</rdfs:description>
<rdfs:label xml:lang="en">Resource</rdfs:label>
</owl:Class>
</rdf:RDF>
<!-- Generated by the OWL API (version 4.2.1.20160306-0033) https://github.com/owlcs/owlapi -->