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orthOntology_v3_a.ttl
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### TODO Improvement of the draft by includins labels and comments/definitions + possible alingnments with existing ontologies
### TODO review correctness of modifications
@prefix : <http://purl.org/net/orth#> .
@prefix up: <http://purl.uniprot.org/core/> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix pav: <http://purl.org/pav/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix orth: <http://purl.org/net/orth#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@base <http://purl.org/net/orth> .
<http://purl.org/net/orth> rdf:type owl:Ontology ;
dct:title "Orthology Ontology"@en ;
dct:description "The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein-centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinent to represent the information from various orthology databases in a homogeneous way."@en ;
owl:versionIRI <http://purl.org/net/orth/3.0> ;
owl:versionInfo """This ontology is the third version of the orthology ontology first published in 2015 and available at http://purl.bioontology.org/ontology/ORTH .
@authors T.M. de Farias, H. Chiba, J.T. Fernandez-Breis, E. Antezana, D. Kuznetsov, C. Dessimoz and F. Villiers."""@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 .
### http://www.w3.org/2004/02/skos/core#altLabel
<http://www.w3.org/2004/02/skos/core#altLabel> rdf:type owl:AnnotationProperty ;
rdfs:comment "The range of skos:altLabel is the class of RDF plain literals."@en ,
"skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties."@en ;
rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
rdfs:label "alternative label"@en ;
<http://www.w3.org/2004/02/skos/core#definition> "An alternative lexical label for a resource."@en ;
<http://www.w3.org/2004/02/skos/core#example> "Acronyms, abbreviations, spelling variants, and irregular plural/singular forms may be included among the alternative labels for a concept. Mis-spelled terms are normally included as hidden labels (see skos:hiddenLabel)."@en ;
rdfs:subPropertyOf rdfs:label .
### http://www.w3.org/2004/02/skos/core#definition
<http://www.w3.org/2004/02/skos/core#definition> rdf:type owl:AnnotationProperty ;
rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
rdfs:label "definition"@en ;
<http://www.w3.org/2004/02/skos/core#definition> "A statement or formal explanation of the meaning of a concept."@en ;
rdfs:subPropertyOf <http://www.w3.org/2004/02/skos/core#note> .
### http://www.w3.org/2004/02/skos/core#example
<http://www.w3.org/2004/02/skos/core#example> rdf:type owl:AnnotationProperty ;
rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
rdfs:label "example"@en ;
<http://www.w3.org/2004/02/skos/core#definition> "An example of the use of a concept."@en ;
rdfs:subPropertyOf <http://www.w3.org/2004/02/skos/core#note> .
### http://www.w3.org/2004/02/skos/core#note
<http://www.w3.org/2004/02/skos/core#note> rdf:type owl:AnnotationProperty ;
rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
rdfs:label "note"@en ;
<http://www.w3.org/2004/02/skos/core#definition> "A general note, for any purpose."@en ;
<http://www.w3.org/2004/02/skos/core#scopeNote> "This property may be used directly, or as a super-property for more specific note types."@en .
### http://www.w3.org/2004/02/skos/core#prefLabel
<http://www.w3.org/2004/02/skos/core#prefLabel> rdf:type owl:AnnotationProperty ;
rdfs:comment "A resource has no more than one value of skos:prefLabel per language tag, and no more than one value of skos:prefLabel without language tag."@en ,
"The range of skos:prefLabel is the class of RDF plain literals."@en ,
"""skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise
disjoint properties."""@en ;
rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
rdfs:label "preferred label"@en ;
<http://www.w3.org/2004/02/skos/core#definition> "The preferred lexical label for a resource, in a given language."@en ;
rdfs:subPropertyOf rdfs:label .
### http://www.w3.org/2004/02/skos/core#scopeNote
<http://www.w3.org/2004/02/skos/core#scopeNote> rdf:type owl:AnnotationProperty ;
rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
rdfs:label "scope note"@en ;
<http://www.w3.org/2004/02/skos/core#definition> "A note that helps to clarify the meaning and/or the use of a concept."@en ;
rdfs:subPropertyOf <http://www.w3.org/2004/02/skos/core#note> .
#################################################################
# Object Properties
#################################################################
### http://purl.obolibrary.org/obo/CDAO_0000148
obo:CDAO_0000148 rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf obo:CDAO_0000178 ;
rdfs:domain obo:CDAO_0000012 ;
rdfs:range obo:CDAO_0000140 ;
rdfs:comment "The property links a rooted tree to the specific node that represents the unique root of the tree."@en ;
rdfs:label "has_Root"^^xsd:string .
### http://purl.obolibrary.org/obo/CDAO_0000178
obo:CDAO_0000178 rdf:type owl:ObjectProperty ;
owl:inverseOf obo:CDAO_0000194 ;
rdfs:comment "Generic 'has' property."@en ;
rdfs:label "has"^^xsd:string .
### http://purl.obolibrary.org/obo/CDAO_0000194
obo:CDAO_0000194 rdf:type owl:ObjectProperty ;
rdfs:label "part_of"^^xsd:string .
### http://purl.obolibrary.org/obo/RO_0001018
obo:RO_0001018 rdf:type owl:ObjectProperty ;
rdfs:comment "This property was simplified. Original range and domain were removed due to be highly abstracted because it is well-know the domain of discourse: orthology databases. The rage restriction of this property is defined as a class restriction in (e.g.: orth:Gene)."@en ;
rdfs:label "contained in"@en .
### http://purl.obolibrary.org/obo/RO_0002162
obo:RO_0002162 rdf:type owl:ObjectProperty ;
rdfs:comment "Connects a biological entity to its taxon of origin."@en ;
rdfs:label "in taxon"@en .
### http://purl.obolibrary.org/obo/RO_0002350
obo:RO_0002350 rdf:type owl:ObjectProperty ;
owl:inverseOf obo:RO_0002351 ;
rdfs:comment "Is member of is a mereological relation between a item and a collection."@en ;
rdfs:isDefinedBy "http://purl.obolibrary.org/obo/ro.owl" ;
rdfs:label "member of"@en .
### http://purl.org/net/orth#hasAncestralEvolutionaryEvent
orth:hasAncestralEvolutionaryEvent rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf orth:hasEvolutionaryEvent ;
rdfs:comment "A property of a homology relation (e.g.: \"inparalogy relation\") to state an ancestral evolutionary event. An ancestral evolutionary event is an event that precedes another evolutionary event. For example, a speciation event before a duplication event."@en ;
rdfs:label "has ancestral evolutionary event"@en .
### http://purl.org/net/orth#hasCoOrthologousMember
orth:hasCoOrthologousMember rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf obo:RO_0002351 ;
rdfs:domain orth:CoOrthologyRelation ;
rdfs:range orth:SequenceUnit ;
rdfs:comment "A property to define the membership of a sequence unit into a co-orthology relation."@en ;
rdfs:label "has co-orthologous member"@en .
### http://purl.org/net/orth#hasDescendantEvolutionaryEvent
orth:hasDescendantEvolutionaryEvent rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf orth:hasEvolutionaryEvent ;
rdfs:comment "A property of a homology relation (e.g.: \"outparalogy relation\") to state a descendant evolutionary event. A descendant evolutionary event is an event that occurs after another evolutionary event. For example, a speciation event after a duplication event."@en ;
rdfs:label "has descendant evolutionary event"@en .
### http://purl.org/net/orth#hasEvolutionaryEvent
orth:hasEvolutionaryEvent rdf:type owl:ObjectProperty ;
rdfs:domain [ rdf:type owl:Class ;
owl:unionOf ( orth:HomologsCluster
orth:OrthologyRelation
orth:ParalogyRelation
)
] ;
rdfs:range obo:CDAO_0000064 ;
rdfs:comment "A property of a homology relation (e.g.: \"paralogy relation\") to state an evolutionary event such as a duplication or a speciation event."@en ;
rdfs:label "has evolutionary event"@en .
### http://purl.org/net/orth#hasHomolog
orth:hasHomolog rdf:type owl:ObjectProperty ;
rdf:type owl:SymmetricProperty ;
rdfs:domain orth:SequenceUnit ;
rdfs:range orth:SequenceUnit ;
rdfs:comment "Homologous pairwise relation between sequence units (e.g.: genes, proteins or gene regions). For example, A Gene(A) hasHomolog Gene(B). This property can be materialized or inferred by applying a logical rule."@en ;
rdfs:label "has homolog"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "is homologous to"@en .
### http://purl.org/net/orth#hasHomologousMember
orth:hasHomologousMember rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf obo:RO_0002351 ;
owl:inverseOf orth:isHomologousMember ;
rdfs:domain [ rdf:type owl:Class ;
owl:unionOf ( orth:HomologsCluster
orth:HomologyRelation
)
] ;
rdfs:range [ rdf:type owl:Class ;
owl:unionOf ( orth:HomologsCluster
orth:SequenceUnit
)
] ;
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#hasHomologyData
orth:hasHomologyData rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf obo:CDAO_0000178 ;
owl:inverseOf orth:inDataset ;
rdfs:domain orth:OrthologyDataset ;
rdfs:range [ rdf:type owl:Class ;
owl:unionOf ( orth:HomologsCluster
orth:HomologyRelation
)
] ;
rdfs:comment "Inverse property of inDataset. It permits to retrieve the clusters or homology relations included in a particular dataset."@en ;
rdfs:label "has homology data"@en .
### http://purl.org/net/orth#hasInparalogousMember
orth:hasInparalogousMember rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf obo:RO_0002351 ;
rdfs:domain orth:CoOrthologyRelation ;
rdfs:range orth:InparalogyRelation ;
rdfs:comment "A property to define the membership of a in-paralogy relation into co-orthology relation."@en ;
rdfs:label "has inparalogous member"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "has in-paralogous member"@en .
### http://purl.org/net/orth#hasLeastDivergedOrtholog
orth:hasLeastDivergedOrtholog rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf orth:hasOrtholog ;
rdf:type owl:SymmetricProperty ;
rdfs:domain orth:SequenceUnit ;
rdfs:range orth:SequenceUnit ;
rdfs:comment "Least diverged orthologs (LDOs) are the genes in two different organisms that have diverged the least since their common ancestor and are most likely to retain the greatest functional similarities."@en ;
rdfs:isDefinedBy "http://pantherdb.org/genes/"^^xsd:anyURI ;
rdfs:label "has least diverged ortholog"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "is least divergent ortholog to"@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."@en ;
rdfs:label "has ortholog"@en ,
"is ortholog to"@en .
### http://purl.org/net/orth#hasParalog
orth:hasParalog rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf orth:hasHomolog ;
rdf:type owl:SymmetricProperty ;
rdfs:comment "Paralogous pairwise relation between genes/proteins. For example, a Gene(A) hasParalog Gene(B). This property can be materialized or inferred by applying a logical rule."@en ;
rdfs:label "has paralog"@en ,
"is paralog to"@en .
### http://purl.org/net/orth#hasTaxonomicRange
orth:hasTaxonomicRange rdf:type owl:ObjectProperty ;
rdfs:domain [ rdf:type owl:Class ;
owl:unionOf ( orth:HomologsCluster
orth:OrthologyRelation
orth:ParalogyRelation
)
] ;
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 level"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "has taxonomic range"@en .
### http://purl.org/net/orth#hasXenolog
orth:hasXenolog rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf orth:hasHomolog ;
rdf:type owl:SymmetricProperty ;
rdfs:comment "Xenologous pairwise relation between genes/proteins. For example, a Gene(A) hasXenolog Gene(B)."@en ;
rdfs:label "has xenolog"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "is xenolog to"@en .
### http://purl.org/net/orth#inDataset
orth:inDataset rdf:type owl:ObjectProperty ;
rdfs:domain [ rdf:type owl:Class ;
owl:unionOf ( orth:HomologsCluster
orth:HomologyRelation
)
] ;
rdfs:range orth:OrthologyDataset ;
rdfs:comment "Property that provides the dataset associated with a gene tree node"@en ;
rdfs:label "in dataset"@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://purl.org/net/orth#organism
orth:organism rdf:type owl:ObjectProperty ;
rdfs:domain orth:SequenceUnit ;
rdfs:range orth:Organism ;
rdfs:comment "A sequence unit (e.g.: gene) comes from an organism."@en ;
rdfs:label "in organism"@en .
### http://purl.uniprot.org/core/replaces
up:replaces rdf:type owl:ObjectProperty ;
rdfs:domain up:Taxon ;
rdfs:range up:Taxon ;
rdfs:comment "A resource that is replaced by this resource."^^xsd:string ;
rdfs:label "replaces"@en .
### http://semanticscience.org/resource/SIO_010078
sio:SIO_010078 rdf:type owl:ObjectProperty ;
owl:inverseOf sio:SIO_010079 ;
rdfs:comment "A relation between two objects, in which the first object contains information that is used to produce the second object."@en ;
rdfs:isDefinedBy <http://semanticscience.org/ontology/sio.owl> ;
rdfs:label "encodes"@en .
### http://semanticscience.org/resource/SIO_010079
sio:SIO_010079 rdf:type owl:ObjectProperty ;
rdfs:comment "A relation between two objects, in which the first object is produced from the information contained in the second object."@en ;
rdfs:isDefinedBy <http://semanticscience.org/ontology/sio.owl> ;
rdfs:label "is encoded by"@en .
#################################################################
# Data properties
#################################################################
### http://purl.org/dc/terms/identifier
dct:identifier rdf:type owl:DatatypeProperty ;
rdfs:range xsd:string ;
rdfs:comment "This property is orignally defined in dcterms schema however in the context of the ORTH ontology we define this property as being an OWL datatype property rather than a generic RDF property. This property should be assigned to any individual that have one or more identifiers. For example, uniprot:P01308 dcterms:identifier \"P01308\"."@en ;
rdfs:label "identifier"@en .
### http://purl.org/net/orth#isLeastDivergedOrtholog
orth:isLeastDivergedOrtholog rdf:type owl:DatatypeProperty ;
rdfs:domain orth:OrthologyRelation ;
rdfs:range xsd:boolean ;
rdfs:comment "Least diverged orthologs (LDOs) are the genes in two different organisms that have diverged the least since their common ancestor and are most likely to retain the greatest functional similarities. This property assigns a boolean value to state if an orthology relation is a actually LDO relation."@en ;
rdfs:label "is least diverged ortholog"@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 level at which a given cluster of homologs has been calculated"@en ;
rdfs:label "taxonomic level"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "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 level."@en ;
rdfs:label "taxonomic level identifier"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "tax range id"@en .
### http://purl.org/pav/version
pav:version rdf:type owl:DatatypeProperty ;
rdfs:range xsd:string ;
rdfs:comment """The version number of a resource. This is a freetext string, typical values are \"1.5\" or \"21\". The URI identifying the previous version can be provided using prov:previousVersion.
This property is normally used in a functional way, although PAV does not formally restrict this."""@en ;
rdfs:isDefinedBy "http://purl.org/pav/"@en ;
rdfs:label "Version"@en .
### http://purl.uniprot.org/core/mnemonic
up:mnemonic rdf:type owl:DatatypeProperty ;
rdfs:range xsd:string ;
rdfs:comment "A easy to remember identifier for a UniProtKB entry, but it is not a stable identifier and should not be used by programs to identify entries."@en ,
"A rememberable string that can be used to find entries, not a stable identifier!"^^xsd:string ;
rdfs:label "Mnemonic"^^xsd:string ;
rdfs:seeAlso "http://www.uniprot.org/manual/entry_name" .
#################################################################
# Classes
#################################################################
### http://purl.obolibrary.org/obo/CDAO_0000012
obo:CDAO_0000012 rdf:type owl:Class ;
rdfs:subClassOf [ rdf:type owl:Restriction ;
owl:onProperty obo:CDAO_0000148 ;
owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ;
owl:onClass obo:CDAO_0000140
] ;
rdfs:comment "Tree with a root node, which is the common ancestor to all the nodes in the tree"@en ;
rdfs:label "RootedTree"^^xsd:string .
### http://purl.obolibrary.org/obo/CDAO_0000064
obo:CDAO_0000064 rdf:type owl:Class ;
rdfs:comment "Evolutionary event"@en ;
rdfs:label "cladogeneticChange"^^xsd:string ;
<http://www.w3.org/2004/02/skos/core#altLabel> "clado genetic change"@en .
### http://purl.obolibrary.org/obo/CDAO_0000077
obo:CDAO_0000077 rdf:type owl:Class ;
rdfs:subClassOf obo:CDAO_0000064 ;
rdfs:comment "Evolutionary event that consists on the duplication of a gene"@en ;
rdfs:label "geneDuplication"^^xsd:string ;
<http://www.w3.org/2004/02/skos/core#altLabel> "gene duplication"@en .
### http://purl.obolibrary.org/obo/CDAO_0000121
obo:CDAO_0000121 rdf:type owl:Class ;
rdfs:subClassOf obo:CDAO_0000064 ;
rdfs:comment "Evolutionary event related with the evolution of a gene in different species"@en ;
rdfs:label "speciation"^^xsd:string .
### http://purl.obolibrary.org/obo/CDAO_0000140
obo:CDAO_0000140 rdf:type owl:Class ;
rdfs:comment "Basic unit of graphs and trees. This class was modified from its original definition (with class restrictions) to avoid multiple statements that relates a Node to a Network (e.g.: RootedTree). In its orignal definition, for each created instance of a Node, an additional statement must be defined to declare that a given node belongs to a Network what is quite verbose. However, we know that sub-nodes of a root node must belong to the same given Rooted Tree (e.g.: HOGs). Therefore, no needs to state sub-nodes to be part of a RootedTree."@en ;
rdfs:label "Node"^^xsd:string .
### http://purl.obolibrary.org/obo/NCIT_C14250
obo:NCIT_C14250 rdf:type owl:Class ;
owl:equivalentClass orth:Organism ;
owl:disjointWith up:Taxon ;
rdfs:comment "A living thing, such as an animal, a plant, a bacterium, or a fungus., Any individual living (or previously living) being. EXAMPLE(S): animal, human being."@en ;
rdfs:isDefinedBy "http://purl.obolibrary.org/obo/ncit.owl" ;
rdfs:label "Organism" .
### http://purl.obolibrary.org/obo/SO_0000104
obo:SO_0000104 rdf:type owl:Class ;
owl:equivalentClass orth:Protein ;
rdfs:comment "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation."@en ;
rdfs:isDefinedBy "http://purl.obolibrary.org/obo/so.owl" ;
rdfs:label "polypeptide"^^xsd:string .
### http://purl.obolibrary.org/obo/SO_0000704
obo:SO_0000704 rdf:type owl:Class ;
owl:equivalentClass orth:Gene ;
rdfs:comment "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions."@en ;
rdfs:isDefinedBy "http://purl.obolibrary.org/obo/so.owl" ;
rdfs:label "gene"^^xsd:string .
### http://purl.obolibrary.org/obo/SO_0000831
obo:SO_0000831 rdf:type owl:Class ;
owl:equivalentClass orth:Subgene ;
rdfs:comment "A manufactured term used to allow the parts of a gene to have an is_a path to the root." ;
rdfs:label "gene_member_region"@en .
### http://purl.obolibrary.org/obo/SO_0005855
obo:SO_0005855 rdf:type owl:Class ;
rdfs:comment "A collection of related genes."@en ;
rdfs:label "gene_group"^^xsd:string ;
<http://www.w3.org/2004/02/skos/core#altLabel> "gene group"@en .
### http://purl.org/net/orth#CoOrthologyRelation
orth:CoOrthologyRelation rdf:type owl:Class ;
rdfs:subClassOf orth:HomologyRelation ,
[ owl:intersectionOf ( [ rdf:type owl:Restriction ;
owl:onProperty orth:hasCoOrthologousMember ;
owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ;
owl:onClass orth:SequenceUnit
]
[ rdf:type owl:Restriction ;
owl:onProperty orth:hasInparalogousMember ;
owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ;
owl:onClass orth:InparalogyRelation
]
) ;
rdf:type owl:Class
] ;
rdfs:comment "Co-orthology is a relation defined over three genes, where two of them are inparalogs with respect to the speciation event associated to the third gene. The two inparalogous genes are said to be co-orthologous to the third (out-group) gene."@en ;
rdfs:label "co-orthology relation"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "co-orthologous relation"@en .
### http://purl.org/net/orth#Gene
orth:Gene rdf:type owl:Class ;
rdfs:subClassOf orth:SequenceUnit ,
[ rdf:type owl:Restriction ;
owl:onProperty orth:organism ;
owl:someValuesFrom orth:Organism
] ,
[ rdf:type owl:Restriction ;
owl:onProperty obo:RO_0001018 ;
owl:allValuesFrom sio:SIO_000750
] ;
owl:disjointWith orth:Protein ;
rdfs:comment "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions."@en ;
rdfs:isDefinedBy "http://purl.obolibrary.org/obo/so.owl" ;
rdfs:label "Gene"@en .
### 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:GeneTreeNode
] ,
[ rdf:type owl:Restriction ;
owl:onProperty obo:CDAO_0000178 ;
owl:allValuesFrom orth:GeneTreeNode
] ;
rdfs:comment "A tree whose leaf nodes correspond to sequence units (e.g.: 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 orth:hasEvolutionaryEvent ;
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 homologous sequences"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "Cluster of homologs"@en ,
"homologous group"@en ,
"homologs cluster"@en .
### http://purl.org/net/orth#HomologyRelation
orth:HomologyRelation rdf:type owl:Class ;
rdfs:subClassOf [ rdf:type owl:Restriction ;
owl:onProperty orth:hasHomologousMember ;
owl:allValuesFrom orth:SequenceUnit
] ,
[ rdf:type owl:Restriction ;
owl:onProperty orth:inDataset ;
owl:allValuesFrom orth:OrthologyDataset
] ;
rdfs:comment "This class represents homology relations among sequence units (e.g genes, proteins or gene regions)."@en ;
rdfs:label "homology relation"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "homologous relation"@en .
### http://purl.org/net/orth#InparalogyRelation
orth:InparalogyRelation rdf:type owl:Class ;
rdfs:subClassOf orth:ParalogyRelation ,
[ rdf:type owl:Restriction ;
owl:onProperty orth:hasAncestralEvolutionaryEvent ;
owl:allValuesFrom obo:CDAO_0000121
] ;
rdfs:comment "Inparalogy is a relation defined over a triplet. It involves a pair of genes and a speciation event of reference. A gene pair is an inparalog if they are paralogs and duplicated after the speciation event of reference."@en ;
rdfs:label "inparalogy relation"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "in-paralogous relation"@en ,
"in-paralogy relation"@en ,
"symparalog"@en .
### http://purl.org/net/orth#LeastDivergedOrthologyRelation
orth:LeastDivergedOrthologyRelation rdf:type owl:Class ;
owl:equivalentClass [ rdf:type owl:Restriction ;
owl:onProperty orth:isLeastDivergedOrtholog ;
owl:hasValue "true"^^xsd:boolean
] ;
rdfs:subClassOf orth:OrthologyRelation ;
rdfs:comment "Least diverged orthologs (LDOs) are the genes in two different organisms that have diverged the least since their common ancestor and are most likely to retain the greatest functional similarities. This is a symmetric relation."@en ;
rdfs:isDefinedBy "http://pantherdb.org/genes/"^^xsd:anyURI ;
rdfs:label "least diverged orthology relation"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "least diverged orthologous relation"@en .
### http://purl.org/net/orth#Organism
orth:Organism rdf:type owl:Class ;
rdfs:subClassOf [ rdf:type owl:Restriction ;
owl:onProperty obo:RO_0002162 ;
owl:someValuesFrom up:Taxon
] ;
rdfs:comment "A living being, such as an animal, a plant, a bacterium, or a fungus., Any individual living (or previously living) being. Example: animal, human being. An organim is associated to a taxon such as \"Homo Sapiens\", NCBI taxonomy identifier: 9606."@en ;
rdfs:label "Organism"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "Living being"@en .
### http://purl.org/net/orth#OrthologsCluster
orth:OrthologsCluster rdf:type owl:Class ;
rdfs:subClassOf orth:HomologsCluster ,
[ rdf:type owl:Restriction ;
owl:onProperty orth:hasEvolutionaryEvent ;
owl:allValuesFrom obo:CDAO_0000121
] ;
owl:disjointWith orth:ParalogsCluster ;
rdfs:comment """Set of homologous sequences derived from a speciation event.
"""@en ;
rdfs:label "Cluster of orthologs"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "Cluster of orthologous sequences"@en ,
"Orthologous cluster"@en ,
"group of orthologs"@en .
### http://purl.org/net/orth#OrthologyDataset
orth:OrthologyDataset rdf:type owl:Class ;
rdfs:subClassOf [ rdf:type owl:Restriction ;
owl:onProperty pav:version ;
owl:someValuesFrom xsd:string
] ;
rdfs:comment """Dataset that provides orthology relations including clusters of orthologs, pairwise orthology relations, and so on.
Examples would be the content of resources such as OMA, InParanoid, TreeFam, PhylomeDB and so on. Each release of the resources is different dataset."""@en ;
rdfs:label "Orthology datasource"@en .
### http://purl.org/net/orth#OrthologyRelation
orth:OrthologyRelation rdf:type owl:Class ;
rdfs:subClassOf orth:HomologyRelation ,
[ owl:intersectionOf ( [ rdf:type owl:Restriction ;
owl:onProperty orth:hasTaxonomicRange ;
owl:allValuesFrom orth:TaxonomicRange
]
[ rdf:type owl:Restriction ;
owl:onProperty orth:hasHomologousMember ;
owl:qualifiedCardinality "2"^^xsd:nonNegativeInteger ;
owl:onClass orth:SequenceUnit
]
) ;
rdf:type owl:Class
] ,
[ rdf:type owl:Restriction ;
owl:onProperty orth:hasEvolutionaryEvent ;
owl:allValuesFrom obo:CDAO_0000121
] ;
owl:disjointWith orth:ParalogyRelation ;
rdfs:comment "homology pairwise relation that involves sequences that diverged after a speciation event."@en ;
rdfs:label "orthology relation"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "orthologous relation"@en .
### http://purl.org/net/orth#OutparalogyRelation
orth:OutparalogyRelation rdf:type owl:Class ;
rdfs:subClassOf orth:ParalogyRelation ,
[ rdf:type owl:Restriction ;
owl:onProperty orth:hasDescendantEvolutionaryEvent ;
owl:allValuesFrom obo:CDAO_0000121
] ;
rdfs:comment "Outparalogy is also a relation defined over a pair of genes and a speciation event of reference. This pair are outparalogs if the duplication event through which they are related to each other predates the speciation event of reference."@en ;
rdfs:label "outparalogy relation"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "alloparalog"@en ,
"out-paralogous relation"@en ,
"out-paralogy relation"@en .
### http://purl.org/net/orth#ParalogsCluster
orth:ParalogsCluster rdf:type owl:Class ;
rdfs:subClassOf orth:HomologsCluster ,
[ rdf:type owl:Restriction ;
owl:onProperty orth:hasEvolutionaryEvent ;
owl:allValuesFrom obo:CDAO_0000077
] ;
rdfs:comment "Set of homologous sequences derived from a duplication event"@en ;
rdfs:label "Cluster of paralogs"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "Cluster of paralogous sequences"@en ,
"Paralogs cluster"@en ,
"group of paralogs"@en .
### http://purl.org/net/orth#ParalogyRelation
orth:ParalogyRelation rdf:type owl:Class ;
rdfs:subClassOf orth:HomologyRelation ,
[ owl:intersectionOf ( [ rdf:type owl:Restriction ;
owl:onProperty orth:hasTaxonomicRange ;
owl:allValuesFrom orth:TaxonomicRange
]
[ rdf:type owl:Restriction ;
owl:onProperty orth:hasHomologousMember ;
owl:qualifiedCardinality "2"^^xsd:nonNegativeInteger ;
owl:onClass orth:SequenceUnit
]
) ;
rdf:type owl:Class
] ,
[ rdf:type owl:Restriction ;
owl:onProperty orth:hasEvolutionaryEvent ;
owl:allValuesFrom obo:CDAO_0000077
] ;
rdfs:comment "Homology relation that involves sequences that diverged after a duplication event."@en ;
rdfs:label "paralogy relation"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "paralogous relation"@en .
### http://purl.org/net/orth#Protein
orth:Protein rdf:type owl:Class ;
rdfs:subClassOf orth:SequenceUnit ,
[ rdf:type owl:Restriction ;
owl:onProperty orth:organism ;
owl:someValuesFrom orth:Organism
] ,
[ rdf:type owl:Restriction ;
owl:onProperty obo:RO_0001018 ;
owl:allValuesFrom sio:SIO_000750
] ;
rdfs:comment "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation."@en ;
rdfs:isDefinedBy "http://purl.obolibrary.org/obo/so.owl" ;
rdfs:label "Protein"@en .
### http://purl.org/net/orth#SequenceUnit
orth:SequenceUnit rdf:type owl:Class ;
rdfs:subClassOf 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 "gene region"@en ,
"region of a gene"@en ,
"subgene"@en .
### http://purl.org/net/orth#TaxonomicRange
orth:TaxonomicRange rdf:type owl:Class ;
rdfs:comment "The taxonomic level represents the taxon at which a group of sequences are considered members of the same cluster of orthologs/paralogs"@en ;
rdfs:label "Taxonomic level"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "Taxonomic range"@en .
### http://purl.org/net/orth#XenologyRelation
orth:XenologyRelation rdf:type owl:Class ;
rdfs:subClassOf orth:HomologyRelation ;
rdfs:comment "Gene pairs whose history, since their divergence, includes a horizontal transfer."@en ;
rdfs:isDefinedBy "https://doi.org/10.1093/bioinformatics/btw686"@en ;
rdfs:label "xenology relation"@en ;
<http://www.w3.org/2004/02/skos/core#altLabel> "xenologous relation"@en .
### http://purl.uniprot.org/core/Taxon
up:Taxon rdf:type owl:Class ;
rdfs:subClassOf [ rdf:type owl:Restriction ;
owl:onProperty up:replaces ;
owl:allValuesFrom up:Taxon
] ,
[ rdf:type owl:Restriction ;
owl:onProperty up:mnemonic ;
owl:maxQualifiedCardinality "1"^^xsd:nonNegativeInteger ;
owl:onDataRange xsd:string
] ;
rdfs:comment "An element of a taxonomy for classifying life forms."^^xsd:string ;
rdfs:label "Taxon"^^xsd:string ;
rdfs:seeAlso "http://www.ncbi.nlm.nih.gov/books/NBK54428/" .
### http://semanticscience.org/resource/SIO_000750
sio:SIO_000750 rdf:type owl:Class ;
rdfs:comment "A database is a data store such as relational, hierarchical and graph databases."@en ;
rdfs:label "database"@en .
#############################
####### New concepts and properties for v3.0
###########################
orth:Genome rdf:type owl:Class ;
rdfs:subClassOf
[ rdf:type owl:Restriction ;
owl:onProperty orth:genomeOf ;
owl:someValuesFrom orth:Organism
] ;
rdfs:comment ""@en ;
rdfs:label "Genome"@en .
orth:Pangenome rdf:type owl:Class ;
rdfs:subClassOf
[ rdf:type owl:Restriction ;
owl:onProperty orth:hasGenomeMember ;
owl:someValuesFrom orth:Genome
] ;
rdfs:comment ""@en ;
rdfs:label "Pangenome"@en .
orth:hasGenome rdf:type owl:ObjectProperty ;
rdfs:domain orth:Organism ;
rdfs:range orth:Genome ;
rdfs:comment ""@en ;
rdfs:label "has genome"^^xsd:string .
orth:genomeOf rdf:type owl:ObjectProperty ;
owl:inverseOf orth:hasGenome ;
rdfs:domain orth:Genome ;
rdfs:range orth:Organism ;
rdfs:comment ""@en ;
rdfs:label "is genome of"^^xsd:string .
orth:includesGenome rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf obo:RO_0002524 ;
owl:inverseOf orth:includedInPangenome ;
rdfs:domain orth:Pangenome ;
rdfs:range orth:Genome ;
rdfs:comment ""@en ;
rdfs:label "includes genome"^^xsd:string .
orth:includedInPangenome rdf:type owl:ObjectProperty ;
rdfs:subProperty obo:RO_0002525 ;
owl:inverseOf orth:includesGenome ;
rdfs:domain orth:Genome ;
rdfs:range orth:Pangenome ;
rdfs:comment ""@en ;
rdfs:label "included in pangenome"^^xsd:string .
### http://purl.obolibrary.org/obo/BFO_0000051
obo:BFO_0000051 rdf:type owl:ObjectProperty, owl:TransitiveProperty ;
rdfs:label "has part" ;
rdfs:comment "a core relation that holds between a whole and its part."@en ;
rdfs:isDefinedBy "http://purl.obolibrary.org/obo/ro.owl" .
### http://purl.obolibrary.org/obo/RO_0002351
obo:RO_0002351 rdf:type owl:ObjectProperty, owl:IrreflexiveProperty ;
rdfs:subPropertyOf obo:BFO_0000051 ;
owl:inverseOf obo:RO_0002350 ;
rdfs:label "has member" ;
rdfs:comment "has member is a mereological relation between a collection and an item."@en ;
rdfs:isDefinedBy "http://purl.obolibrary.org/obo/ro.owl" .
### Generated by the OWL API (version 4.2.8.20170104-2310) https://github.com/owlcs/owlapi