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openbiodiv-ontology.ttl
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openbiodiv-ontology.ttl
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## ----Prefix--------------------------------------------------------------
@prefix : <http://openbiodiv.net/> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix pro: <http://purl.org/spar/pro/> .
@prefix scoro: <http://purl.org/spar/scoro/> .
@prefix ti: <http://www.ontologydesignpatterns.org/cp/owl/timeinterval.owl#> .
@prefix tvc: <http://www.essepuntato.it/2012/04/tvc/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix fabio: <http://purl.org/spar/fabio/> .
@prefix dcelements: <http://purl.org/dc/elements/1.1/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix frbr: <http://purl.org/vocab/frbr/core#> .
@prefix prism: <http://prismstandard.org/namespaces/basic/2.0/> .
@prefix doco: <http://purl.org/spar/doco/> .
@prefix po: <http://www.essepuntato.it/2008/12/pattern#> .
@prefix co: <http://purl.org/co/> .
@prefix trt: <http://plazi.org/treatment#> .
@prefix c4o: <http://purl.org/spar/c4o/> .
@prefix dwciri: <http://rs.tdwg.org/dwc/iri/> .
@prefix nomen: <http://www.semanticweb.org/dmitriev/ontologies/2013/8/untitled-ontology-6#> .
@prefix dwc: <http://rs.tdwg.org/dwc/terms/> .
@prefix sro: <http://salt.semanticauthoring.org/ontologies/sro#> .
@prefix deo: <http://purl.org/spar/deo/> .
@prefix pext: <http://proton.semanticweb.org/protonue#> .
@prefix ptop: <http://proton.semanticweb.org/protont#> .
@prefix pkm: <http://proton.semanticweb.org/protonkm#> .
@prefix vcard: <http://www.w3.org/2006/vcard/ns#> .
@prefix dbr: <http://dbpedia.org/resource/> .
@prefix org: <http://www.w3.org/ns/org#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix lucene: <http://www.ontotext.com/connectors/lucene#> .
@prefix inst: <http://www.ontotext.com/connectors/lucene/instance#> .
@prefix dbo: <http://dbpedia.org/ontology/> .
@prefix vs: <http://www.w3.org/2003/06/sw-vocab-status/ns#> .
@prefix dwcattributesns: <http://rs.tdwg.org/dwc/terms/attributes/> .
## ----Ontology Metadata---------------------------------------------------
:openbiodiv-ontology rdf:type owl:Ontology ;
owl:versionInfo "1.0.1" ;
rdfs:comment "You are free to create derivative work as long as you cite the original authors." ;
dcelements:title "The Open Biodiversity Knowledge Management System Ontology" ;
dcelements:subject "Biodiversity Informatics" ;
rdfs:label "OpenBiodiv Ontology" ;
dcelements:creator "Viktor Senderov, Kiril Simov" ;
dcelements:license "CC-BY license version 4.0" ;
owl:imports <http://purl.org/spar/fabio/> .
## ------------------------------------------------------------------------
frbr:realization owl:inverseOf frbr:realizationOf.
## ----http://www.essepuntato.it/2008/12/pattern#contains------------------
po:contains rdf:type owl:ObjectProperty ;
owl:inverseOf po:isContainedBy ;
rdfs:domain po:Structured ;
rdfs:comment "A structured element contains another generic element."@en ;
rdfs:label "contains"@en .
## ----http://www.essepuntato.it/2008/12/pattern#isContainedBy-------------
po:isContainedBy rdf:type owl:ObjectProperty ;
rdfs:comment "An element that is contained by another structured element."@en ;
rdfs:label "is contained by"@en .
## ----http://www.essepuntato.it/2008/12/pattern#Structured----------------
po:Structured rdf:type owl:Class ;
rdfs:subClassOf po:Pattern ;
rdfs:comment "The class of elements that can contain other elements."@en ;
rdfs:label "structured element"@en .
## ----http://www.essepuntato.it/2008/12/pattern#Pattern-------------------
po:Pattern rdf:type owl:Class ;
rdfs:subClassOf owl:Thing ;
rdfs:comment "A structural pattern is an atomic component of a document, that is able to capture a recurrent and well known structure of a document. Any entity belonging to this class is compliant with exactly one structural pattern."@en ;
rdfs:label "pattern-based element"@en .
## ----http://proton.semanticweb.org/protonue#Mention----------------------
:Mention rdf:type owl:Class ;
rdfs:seeAlso pext:Mention ;
rdfs:subClassOf deo:DiscourseElement ;
rdfs:comment "An area of a document that can be considered a mention of something."@en ;
rdfs:label "Mention" .
## ------------------------------------------------------------------------
ptop:Statement rdf:type owl:Class ;
rdfs:comment "A message that is stated or declared; a communication (oral or written), setting forth particulars or facts, etc; \"according to his statement he was in London on that day\". WordNet 1.7.1"@en ;
rdfs:label "Statement"@en .
## ----http://xmlns.com/foaf/0.1/Agent-------------------------------------
foaf:Agent rdf:type owl:Class ;
rdfs:comment "An agent (eg. person, group, software or physical artifact)." ;
rdfs:label "Agent" ;
vs:term_status "stable" .
## ----http://proton.semanticweb.org/protonkm#mentions---------------------
:mentions
rdf:type owl:ObjectProperty ;
rdfs:comment "A direct link between an information resource, like a document or a section and an entity." ;
rdfs:domain :Mention ;
rdfs:label "mentions" .
## ----http://openbiodiv.net/contains--------------------------------------
:contains rdf:type owl:ObjectProperty, owl:TransitiveProperty ;
rdfs:label "OpenBiodiv contains" ;
rdfs:subPropertyOf po:contains.
:isContainedBy rdf:type owl:ObjectProperty, owl:TransitiveProperty ;
rdfs:label "OpenBiodiv is contained by" ;
rdfs:subPropertyOf po:isContainedBy.
## ----http://openbiodiv.net/Publisher-------------------------------------
:Publisher rdf:type owl:Class ;
rdfs:label "Publisher"@en ;
rdfs:comment "The publisher of a journal, a type of `foaf:Agent`."@en ;
rdfs:subClassOf foaf:Agent .
## ----http://openbiodiv.net/TaxonomicArticle------------------------------
:TaxonomicArticle rdf:type owl:Class ;
rdfs:subClassOf fabio:JournalArticle ;
rdfs:label "Taxonomic Article"@en .
## ----http://openbiodiv.net/Treatment-------------------------------------
:Treatment a owl:Class ;
rdfs:subClassOf deo:DiscourseElement ,
[ rdf:type owl:Restriction ;
owl:onProperty :isContainedBy ;
owl:someValuesFrom :TaxonomicArticle ] ;
rdfs:label "Taxonomic Treatment"@en ;
rdfs:comment "A rhetorical element of a taxonomic publication, where taxon
circumscription takes place."@en ;
rdfs:comment "Таксономично пояснение или само Пояснение е риторчна част
от таксономичната статия, където се случва описанието
на дадена таксономична концепция."@bg .
## ----http://openbiodiv.net/NomenclatureSection---------------------------
:NomenclatureSection a owl:Class ;
rdfs:subClassOf deo:DiscourseElement,
[ rdf:type owl:Restriction ;
owl:onProperty :isContainedBy ;
owl:someValuesFrom :Treatment ] ;
rdfs:label "Nomenclature Section"@en ;
rdfs:comment "A section of a taxonomic treatment, containing the scientific
name of the taxon described by the treatment, and citations to previous
descriptions, designations of type-genus, and type-species,
and other information."@en .
## ----http://openbiodiv.net/NomenclatureHeading---------------------------
:NomenclatureHeading a owl:Class ;
rdfs:subClassOf deo:DiscourseElement ,
[ rdf:type owl:Restriction ;
owl:onProperty :isContainedBy ;
owl:someValuesFrom :NomenclatureSection ] ;
rdfs:label "Nomenclature Heading"@en ;
rdfs:comment "Inside the taxonomic nomenclature section, we have the treatment
title (name of the taxon)."@en .
## ----http://openbiodiv.net/NomenclatureCitationsList---------------------
:NomenclatureCitationsList a owl:Class ;
rdfs:subClassOf deo:DiscourseElement ,
[ rdf:type owl:Restriction ;
owl:onProperty :isContainedBy ;
owl:someValuesFrom :NomenclatureSection ] ;
rdfs:label "Nomenclature Citations List"@en ;
rdfs:comment "A section in a treatment that includes the citation of one or
several previous treatments of the taxon."@en .
## ----http://openbiodiv.net/BiologySection--------------------------------
:BiologySection a owl:Class ;
rdfs:subClassOf deo:DiscourseElement,
[ rdf:type owl:Restriction ;
owl:onProperty :isContainedBy ;
owl:someValuesFrom :Treatment ] ;
rdfs:label "Biology Section"@en .
## ----http://openbiodiv.net/DescriptionSection----------------------------
:DescriptionSection a owl:Class ;
rdfs:subClassOf deo:DiscourseElement,
[ rdf:type owl:Restriction ;
owl:onProperty :isContainedBy ;
owl:someValuesFrom :Treatment ] ;
rdfs:label "Description Section"@en .
## ----http://openbiodiv.net/DiagnosisSection------------------------------
:DiagnosisSection a owl:Class ;
rdfs:subClassOf deo:DiscourseElement,
[ rdf:type owl:Restriction ;
owl:onProperty :isContainedBy ;
owl:someValuesFrom :Treatment ] ;
rdfs:label "Diagnosis Section"@en .
## ----http://openbiodiv.net/DistributionSection---------------------------
:DistributionSection a owl:Class ;
rdfs:subClassOf deo:DiscourseElement,
[ rdf:type owl:Restriction;
owl:onProperty :isContainedBy;
owl:someValuesFrom :Treatment ];
rdfs:label "Distribution Section"@en.
## ----http://openbiodiv.net/EtymologySection------------------------------
:EtymologySection a owl:Class ;
rdfs:subClassOf deo:DiscourseElement,
[ rdf:type owl:Restriction ;
owl:onProperty :isContainedBy ;
owl:someValuesFrom :Treatment ] ;
rdfs:label "Etymology Section"@en .
## ----http://openbiodiv.net/TaxonomicKey----------------------------------
:TaxonomicKey a owl:Class;
rdfs:subClassOf deo:DiscourseElement,
[ rdf:type owl:Restriction;
owl:onProperty :isContainedBy;
owl:someValuesFrom :TaxonomicArticle ];
rdfs:label "Taxonomic Key"@en.
## ----http://openbiodiv.net/MaterialsExamined-----------------------------
:MaterialsExamined a owl:Class ;
rdfs:subClassOf deo:DiscourseElement ,
[ rdf:type owl:Restriction ;
owl:onProperty :isContainedBy ;
owl:someValuesFrom :Treatment ] ;
rdfs:label "Materials Examined"@en .
## ----http://openbiodiv.net/TaxonomicChecklist----------------------------
:TaxonomicChecklist a owl:Class ;
rdfs:subClassOf deo:DiscourseElement ,
[ rdf:type owl:Restriction ;
owl:onProperty :isContainedBy ;
owl:someValuesFrom :TaxonomicArticle ] ;
rdfs:label "Taxonomic Checklist"@en ;
rdfs:comment "A section in a taxonomic article."@en.
## ----http://openbiodiv.net/TaxonomicNameUsage----------------------------
:TaxonomicNameUsage rdf:type owl:Class ;
rdfs:subClassOf :Mention ;
rdfs:comment "A taxonomic name usage is the mentioning of a taxonomic name
(scientific name, taxonomic concept label, etc.), optionally with
a taxonomic status."@en ;
rdfs:label "Taxonomic Name Usage"@en .
## ----http://rs.tdwg.org/dwc/iri/taxonomicStatus--------------------------
dwciri:taxonomicStatus rdf:type owl:ObjectProperty ;
rdfs:label "taxonomic status"@en ;
rdfs:comment "the IRI version of the DwC term taxonomic status"@en .
## ----http://openbiodiv.net/TaxonomicName---------------------------------
:TaxonomicName rdf:type owl:Class ;
skos:prefLabel "Taxonomic Name"@en ;
skos:altLabel "Biological Name"@en ;
owl:equivalentClass nomen:NOMEN_0000030 .
## ----http://openbiodiv.net/ScientificName--------------------------------
:ScientificName rdf:type owl:Class ;
rdfs:subClassOf :TaxonomicName ;
rdfs:label "Scientific Name"@en ;
owl:equivalentClass nomen:NOMEN_0000036 .
## ----http://openbiodiv.net/LatinName-------------------------------------
:LatinName rdf:type owl:Class ;
rdfs:subClassOf :ScientificName ;
skos:prefLabel "Latinized Scientific Name"@en ;
skos:altLabel "Linnaean Name"@en .
## ----http://openbiodiv.net/TaxonomicConceptLabel-------------------------
:TaxonomicConceptLabel rdf:type owl:Class ;
rdfs:subClassOf :LatinName ;
rdfs:label "Taxon Concept Label"@en ;
rdfs:comment "A taxon concept label is a taxonomic name
usage accompanied by an additional part, consisting of 'sec.' + an identifier
or a literature reference of a work containing the expression of a taxon concept
(treatment)."@en .
## ----http://openbiodiv.net/OTU_Id----------------------------------------
:OTU_Id rdf:type owl:Class ;
rdfs:subClassOf :ScientificName ;
rdfs:label "Operational Taxonomic Unit Identifier"@en ;
rdfs:comment "The identifier of an Operational Taxonomic Unit, such as
BOLD BIN or a Unite SH ID"@en .
## ----http://openbiodiv.net/VernacularName--------------------------------
:VernacularName a owl:Class ;
rdfs:subClassOf :TaxonomicName ;
rdfs:label "Vernacular Name"@en ;
owl:equivalentClass nomen:NOMEN_0000037 .
## ----http://rs.tdwg.org/dwc/iri/nameAccordingTo--------------------------
dwciri:nameAccordingTo rdf:type owl:ObjectProperty ;
rdfs:label "name according to"@en ;
rdfs:comment "the IRI version of dwc:nameAccordingTo"@en .
## ----http://openbiodiv.net/nameAccordingTo-------------------------------
:nameAccordingTo rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf dwciri:nameAccordingTo ;
skos:prefLabel "OpenBiodiv name according to"@en ;
skos:altLabel "sensu"@en ;
rdfs:range frbr:Expression ;
rdfs:domain :TaxonomicConceptLabel ;
rdfs:comment "The reference to the source in which the specific taxonomic
concept circumscription is defined or implied - traditionally signified by
the Latin 'sensu' or 'sec.'' (from secundum, meaning 'according to').
For taxa that are relevantly circumscribed by identifications, a reference
to the keys, monographs, experts and other sources should be given. Should
only be used with IRI's"@en .
## ----http://openbiodiv.net/relatedName-----------------------------------
:relatedName rdf:type owl:ObjectProperty, owl:TransitiveProperty, owl:ReflexiveProperty ;
rdfs:label "has related name"@en ;
rdfs:domain :TaxonomicName ;
rdfs:range :TaxonomicName ;
rdfs:comment "'has related name' is an object property that we
use in order to indicate that two taxonomic names are related somehow. This
relationship is purposely vague as to encompass all situations where two
taxonomic names co-occur in a text. It is transitive and reflexive."@en.
## ----http://openbiodiv.net/replacementName-------------------------------
:replacementName rdf:type owl:ObjectProperty ,
owl:TransitiveProperty ;
rdfs:label "has replacement name"@en ;
rdfs:domain :LatinName ;
rdfs:range :LatinName ;
rdfs:comment "This is a uni-directional property. Its meaning
is that one Linnaean name links to a different Linnaean name via the
usage of this property, then the object name is more accurate and should be
preferred given the information that system currently holds. This property is only
defined for Linnaean names."@en.
## ----http://rs.tdwg.org/dwc/terms/Taxon----------------------------------
<http://rs.tdwg.org/dwc/terms/Taxon> rdf:type owl:Class ;
dcelements:description "Example: The genus Truncorotaloides as published by Brönnimann et al. in 1953 in the Journal of Paleontology Vol. 27(6) p. 817-820."@en ;
dcelements:hasVersion <http://rs.tdwg.org/dwc/terms/history/#Taxon-2014-10-23> ;
dcelements:issued "2008-11-19" ;
dcelements:modified "2014-10-23" ;
dcelements:replaces <http://rs.tdwg.org/dwc/terms/Taxon-2009-09-21> ;
dwcattributesns:abcdEquivalence "no simple equivalent in ABCD" ;
dwcattributesns:decision <http://rs.tdwg.org/dwc/terms/history/decisions/#Decision-2014-10-26_15> ;
dwcattributesns:status "recommended" ;
rdfs:comment "A group of organisms (sensu http://purl.obolibrary.org/obo/OBI_0100026) considered by taxonomists to form a homogeneous unit."@en ;
rdfs:isDefinedBy <http://rs.tdwg.org/dwc/terms/> ;
rdfs:label "Taxon"@en .
## ----http://openbiodiv.net/OperationalTaxonomicUnit----------------------
:OperationalTaxonomicUnit rdf:type owl:Class ;
rdfs:subClassOf skos:Concept, fabio:Work ;
rdfs:label "Operational Taxonomic Unit"@en ;
rdfs:comment "A superclass for all kinds of taxonomic hypothesis"@en .
## ----http://openbiodiv.net/TaxonomicConcept------------------------------
:TaxonomicConcept rdf:type owl:Class ;
owl:equivalentClass dwc:Taxon ;
rdfs:subClassOf :OperationalTaxonomicUnit ,
[ rdf:type owl:Restriction ;
owl:onProperty :taxonomicConceptLabel ;
owl:minCardinality "1" ] ;
rdfs:comment "A taxonomic concept in the sense of Berendsohn"@en .
## ----http://rs.tdwg.org/dwc/iri/scientificName---------------------------
dwciri:scientificName rdf:type owl:ObjectProperty ;
rdfs:label "has scientific name"@en;
rdfs:comment "the IRI version of dwc:scientificName"@en .
## ----http://openbiodiv.net/taxonomicName---------------------------------
:taxonomicName rdf:type owl:ObjectProperty ;
rdfs:label "has OpenBiodiv taxonomic name"@en ;
rdfs:domain :TaxonomicConcept ;
rdfs:range :TaxonomicName .
## ----http://openbiodiv.net/scientificName--------------------------------
:scientificName rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf :taxonomicName, dwciri:scientificName ;
rdfs:label "has OpeonBiodiv scientific name"@en ;
rdfs:domain :TaxonomicConcept ;
rdfs:range :ScientificName .
## :vernacularName rdf:type owl:ObjectProperty ;
## ----http://openbiodiv.net/taxonomicConceptLabel-------------------------
:taxonomicConceptLabel rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf :scientificName ;
rdfs:label "has taxon concept label"@en ;
rdfs:domain :TaxonomicConcept ;
rdfs:range :TaxonomicConceptLabel .
## ----http://openbiodiv.net/has_OTU_id------------------------------------
:has_OTU_Id rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf :scientificName ;
rdfs:label "has OTU Id"@en ;
rdfs:domain :TaxonomicConcept ;
rdfs:range :OTU_Id .
## ----http://openbiodiv.net/RCC5RelationshipTerms-------------------------
:RCC5Dictionary rdf:type owl:Class ;
rdfs:subClassOf skos:ConceptScheme ,
[ rdf:type owl:Restriction ;
owl:onProperty fabio:isSchemeOf ;
owl:allValuesFrom :RCC5Relation] ;
rdfs:label "Dictionary of RCC5 Relations"@en .
## ----http://openbiodiv.net/RCC5Relation----------------------------------
:RCC5Relation rdf:type owl:Class ;
rdfs:subClassOf skos:Concept ;
rdfs:subClassOf [ rdf:type owl:Restriction ;
owl:onProperty <http://www.w3.org/2004/02/skos/core#inScheme> ;
owl:someValuesFrom :RCC5Dictionary ] ;
rdfs:label "RCC5 Relation"@en ;
rdfs:comment "The of RCC 5 relation, e.g. 'partially overlaps'"@en .
## ----http://openbiodiv.net/RCC5Statement---------------------------------
:RCC5Statement rdf:type owl:Class ;
rdfs:subClassOf ptop:Statement ;
rdfs:label "RCC5 Statement" ;
rdfs:comment "A statement of RCC-5 relationship" .
## ----http://openbiodiv.net/rcc5Property----------------------------------
:rcc5Property rdf:Type owl:ObjectProperty ;
rdfs:domain :RCC5Statement .
## ----http://openbiodiv.net/rcc5fromRegion--------------------------------
:rcc5fromRegion rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf :rcc5Property ;
rdfs:label "from region" ;
rdfs:comment "Connects to the RCC5 statement to the originating region"@en .
## ----http://openbiodiv.net/rcc5toRegion----------------------------------
:rcc5toRegion rdf:type owl:ObjectProperty ;
rdfs:label "to region" ;
rdfs:subPropertyOf :rcc5Property ;
rdfs:comment "Connects to the RCC5 statement to the target region"@en .
## ----http://openbiodiv.net/rcc5RelationType------------------------------
:rcc5RelationType rdf:type owl:ObjectProperty ;
rdfs:label "relation type" ;
rdfs:subPropertyOf :rcc5Property ;
rdfs:range :RCC5Relation ;
rdfs:comment "Connects an RCC-5 statement to the type of RCC-5 relation between the regions."@en .
## ----http://openbiodiv.net/rcc5AccordingTo-------------------------------
:rcc5AccrodingTo rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf :rcc5Property ;
rdfs:label "RCC5 statement according to" ;
rdfs:range frbr:Expression ;
rdfs:comment "In which publication was the statement made"@en .
## ----http://openbiodiv.net/TaxonomicStatusDictionary---------------------
:TaxonomicStatusDictionary rdf:type owl:Class ;
rdfs:subClassOf <http://www.w3.org/2004/02/skos/core#ConceptScheme> ,
[ rdf:type owl:Restriction ;
owl:onProperty fabio:isSchemeOf ;
owl:allValuesFrom :TaxonomicStatus] ;
rdfs:label "Dictionary of Taxonomic Statuses" ;
fabio:hasDiscipline <http://dbpedia.org/page/Taxonomy_(biology)> .
## ----http://openbiodiv.net/TaxonomicStatus-------------------------------
:TaxonomicStatus rdf:type owl:Class ;
rdfs:subClassOf skos:Concept ;
rdfs:subClassOf [ rdf:type owl:Restriction ;
owl:onProperty <http://www.w3.org/2004/02/skos/core#inScheme> ;
owl:someValuesFrom :TaxonomicStatusDictionary ] ;
rdfs:label "Taxonomic Status Term"@en ;
rdfs:comment "The status following a taxonomic name usage in a taxonomic
manuscript, i.e. 'n. sp.',
'comb. new',
'sec. Franz (2017)', etc"@en .