#
# Prefixes
#
@prefix dce: .
@prefix dct: .
@prefix foaf: .
@prefix owl: .
@prefix rdfs: .
@prefix skos: .
@prefix unicore: .
@prefix xsd: .
@prefix snomedct: .
@prefix agent: .
@prefix event: .
@prefix fos: .
@prefix clinskosch: .
@prefix orgism: .
orgism:
a owl:Ontology;
dce:title """Organism"""@en;
dce:creator """Hans Cools, Pieterjan De Potter, Pedro Debevere"""@en;
dce:publisher """Agfa Healthcare/Belgium, IBBT/Belgium, Multimedia Lab/Ghent University/Belgium"""@en;
dce:description """Formal general description of organisms, excluding humans, and the roles they can play."""@en;
dce:format """OWL Full"""@en;
dce:identifier """orgism"""@en;
dce:language """English"""@en.
#
# Classes
#
orgism:Organism
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:label """organism"""@en;
skos:definition """Any living thing."""@en;
skos:note """superclass can be organism in a more general way: any complex thing having properties and functions determined not only by the properties of its individual parts, but by the character of the whole that they compose and by the relations of the parts to the whole."""@en;
rdfs:subClassOf foaf:Agent, dct:PhysicalResource;
owl:disjointWith unicore:Taxon;
rdfs:subClassOf [
a owl:Restriction;
owl:onProperty orgism:beingState;
owl:hasValue orgism:alive
];
skos:exactMatch [
a skos:Concept;
skos:inScheme clinskosch:sct20080731;
skos:notation "410607006"^^clinskosch:sctDT
].
orgism:Life
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:label """life"""@en;
skos:definition """The process of being alive."""@en;
rdfs:subClassOf event:Process, event:Existence.
orgism:alive
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:label """alive"""@en;
skos:definition """State of being alive."""@en;
skos:note """Up till now no satisfying definition."""@en.
orgism:dead
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:label """dead"""@en;
skos:definition """State of being not alive anymore."""@en;
rdfs:subClassOf snomedct:SCTID_419099009;
skos:exactMatch [
a skos:Concept;
skos:inScheme clinskosch:sct20080731;
skos:notation "419099009"^^clinskosch:sctDT
];
skos:exactMatch [
a skos:Concept;
skos:inScheme clinskosch:icpc2;
skos:notation "A96"^^clinskosch:icpc2DT
];
skos:exactMatch [
a skos:Concept;
skos:inScheme clinskosch:icd10;
skos:notation "R99"^^clinskosch:icd10DT
].
orgism:IndividualLife
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:label """individual life"""@en;
skos:definition """Life of an organism after birth."""@en;
rdfs:subClassOf orgism:Life.
#Following elements provided by http://purl.uniprot.org/core/
#orgism:Taxon
# a rdfs:Class;
# rdfs:isDefinedBy orgism:;
# rdfs:label """taxonomic position"""@en;
# skos:definition """Position of an organism in the hierarchy of the biological classification or taxonomy."""@en;
# a rdfs:Class.
#orgism:Domain down to orgism:Subspecies rdfs:subClassOf orgism:TaxonRank.
orgism:DevelopmentState
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:label """development state"""@en;
skos:definition """Any state of development."""@en.
orgism:immature
rdfs:isDefinedBy orgism:;
rdfs:label """immature"""@en;
skos:definition """Property of being biologically not full-grown."""@en;
a orgism:DevelopmentState.
orgism:mature
rdfs:isDefinedBy orgism:;
rdfs:label """mature"""@en;
skos:definition """Property of being biologically full-grown, capable of reproduction."""@en;
a orgism:DevelopmentState.
orgism:MatureOrganism
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:label """mature organism"""@en;
skos:definition """Organism being mature."""@en;
rdfs:subClassOf orgism:Organism;
rdfs:subClassOf [
a owl:Restriction;
owl:onProperty orgism:developmentState;
owl:hasValue orgism:mature
].
orgism:ImmatureOrganism
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:label """immature organism"""@en;
skos:definition """Organism being immature."""@en;
rdfs:subClassOf orgism:Organism;
rdfs:subClassOf [
a owl:Restriction;
owl:onProperty orgism:developmentState;
owl:hasValue orgism:immature
].
orgism:PregnantOrganism
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:label """pregnant organism"""@en;
skos:definition """Organism being pregnant."""@en;
rdfs:subClassOf orgism:Organism;
rdfs:subClassOf [
a owl:Restriction;
owl:onProperty orgism:gravidity;
owl:someValuesFrom orgism:pregnant
].
orgism:Gravidity
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:label """gravidity"""@en;
skos:definition """Any state of gravidity."""@en;
owl:oneOf (orgism:pregnant orgism:nonpregnant).
orgism:pregnant
rdfs:isDefinedBy orgism:;
rdfs:label """pregnant"""@en;
skos:definition """State of an organism of having offspring developing in its body."""@en;
a orgism:Gravidity.
orgism:nonpregnant
rdfs:isDefinedBy orgism:;
rdfs:label """nonpregnant"""@en;
skos:definition """State of an organism of not having offspring developing in its body."""@en;
a orgism:Gravidity.
orgism:BiologicalParent
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:label """biological parent"""@en;
skos:definition """First grade living ascendant of any kind."""@en;
rdfs:subClassOf agent:Parent, orgism:MatureOrganism;
rdfs:comment """Organism that produces another."""@en.
orgism:BiologicalAncestry
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:subClassOf agent:Ancestry;
rdfs:subClassOf [
a owl:Restriction;
owl:onProperty foaf:member;
owl:someValuesFrom orgism:BiologicalParent
].
orgism:BiologicalParents
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:subClassOf orgism:BiologicalAncestry.
# restriction: all parents need to have a same biological child
orgism:BiologicalMother
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:label """biological mother"""@en;
skos:definition """Female biological parent."""@en;
rdfs:subClassOf orgism:BiologicalParent;
owl:disjointWith orgism:BiologicalFather.
orgism:BiologicalFather
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:label """biological father"""@en;
skos:definition """Male biological parent."""@en;
rdfs:subClassOf orgism:BiologicalParent.
orgism:BiologicalChild
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:label """biological child"""@en;
skos:definition """First grade living descendant of any kind."""@en;
rdfs:subClassOf agent:Child,
orgism:Organism;
rdfs:comment """Organism that is produced by another."""@en;
rdfs:subClassOf [
a owl:Restriction;
owl:onProperty orgism:hasBiologicalParent;
owl:minCardinality "1"^^xsd:nonNegativeInteger
];
skos:exactMatch [
a skos:Concept;
skos:inScheme clinskosch:sct20080731;
skos:notation "75226009"^^clinskosch:sctDT
].
orgism:BiologicalOffspring
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:subClassOf agent:Offspring;
rdfs:subClassOf [
a owl:Restriction;
owl:onProperty foaf:member;
owl:allValuesFrom orgism:BiologicalChild
].
orgism:BiologicalChildren
a rdfs:Class;
rdfs:isDefinedBy orgism:;
rdfs:subClassOf orgism:BiologicalOffspring.
# restriction: all children need to have a same biological parent
#
# Properties
#
orgism:beingState
a owl:ObjectProperty;
rdfs:isDefinedBy orgism:;
skos:definition """Specifying a state of being of something."""@en;
rdfs:range [owl:oneOf(orgism:alive orgism:dead)].
orgism:lives
a owl:ObjectProperty;
rdfs:isDefinedBy orgism:;
skos:definition """Specifying a life process of an organism."""@en;
rdfs:subPropertyOf event:exists;
rdfs:domain orgism:Organism;
rdfs:range orgism:Life.
orgism:developmentState
a owl:ObjectProperty;
rdfs:isDefinedBy orgism:;
skos:definition """Specifying the state of development of an individual organism."""@en;
rdfs:domain orgism:Organism;
rdfs:range orgism:DevelopmentState.
orgism:gravidity
a owl:ObjectProperty;
rdfs:isDefinedBy orgism:;
skos:definition """Specifying the gravidity of an organism."""@en;
rdfs:domain orgism:Organism;
rdfs:range orgism:Gravidity.
orgism:begins
a owl:DatatypeProperty;
rdfs:isDefinedBy orgism:;
# rdfs:label """birth date"""@en;
skos:definition """Specifying the beginning of a life of an organism as individual."""@en;
skos:note """End of a delivery."""@en;
rdfs:subPropertyOf event:begins;
rdfs:domain orgism:IndividualLife;
rdfs:range xsd:dateTime;
skos:exactMatch [
a skos:Concept;
skos:inScheme clinskosch:sct20080731;
skos:notation "184099003"^^clinskosch:sctDT
].
#orgism:birthTime
# a owl:DatatypeProperty;
# rdfs:isDefinedBy orgism:;
# rdfs:label """birth time"""@en;
# skos:definition """Specifying the time of becoming an individual organism, as the end of the birth action or delivery."""@en;
# rdfs:subPropertyOf orgism:birthDate.
orgism:birthDate
a owl:DatatypeProperty;
rdfs:isDefinedBy orgism:;
skos:definition """Specifying a snapshot an organism is born."""@en;
owl:propertyChainAxiom (orgism:lives orgism:begins); # -> owl:objectPropertyChain?
rdfs:domain orgism:Organism;
rdfs:range xsd:dateTime.
orgism:ends
a owl:DatatypeProperty;
rdfs:isDefinedBy orgism:;
# rdfs:label """died"""@en;
skos:definition """Specifying the end of a life of an organism."""@en;
rdfs:subPropertyOf event:expires;
rdfs:domain orgism:Life;
rdfs:range xsd:dateTime;
skos:exactMatch [
a skos:Concept;
skos:inScheme clinskosch:sct20080731;
skos:notation "399753006"^^clinskosch:sctDT
].
#orgism:deathTime
# a owl:DatatypeProperty;
# rdfs:isDefinedBy orgism:;
# rdfs:label """death time"""@en;
# skos:definition """Specifying the time of ceasing to be an organism."""@en;
# rdfs:subPropertyOf orgism:deathDate.
orgism:deathDate
a owl:DatatypeProperty;
rdfs:isDefinedBy orgism:;
skos:definition """Specifying a snapshot an organism died."""@en;
owl:propertyChainAxiom (orgism:lives orgism:ends);
rdfs:domain orgism:Organism;
rdfs:range xsd:dateTime.
orgism:hasBiologicalParent
a owl:ObjectProperty;
rdfs:isDefinedBy orgism:;
skos:definition """Specifying the first grade ascendent of an organism or group of organisms."""@en;
rdfs:subPropertyOf agent:hasParent;
rdfs:domain [
owl:unionOf(orgism:BiologicalChild orgism:BiologicalChildren)
];
rdfs:range orgism:BiologicalParent.
orgism:biologicalMother
a owl:ObjectProperty, owl:FunctionalProperty;
rdfs:isDefinedBy orgism:;
skos:definition """Specifying the first grade female ascendent of an organism."""@en;
rdfs:subPropertyOf orgism:hasBiologicalParent;
rdfs:domain orgism:BiologicalChild;
rdfs:range orgism:BiologicalMother.
orgism:biologicalFather
a owl:ObjectProperty, owl:FunctionalProperty;
rdfs:isDefinedBy orgism:;
skos:definition """Specifying the first grade male ascendent of an organism."""@en;
rdfs:subPropertyOf orgism:hasBiologicalParent;
rdfs:domain orgism:BiologicalChild;
rdfs:range orgism:BiologicalFather.
orgism:hasBiologicalChild
a owl:ObjectProperty;
rdfs:isDefinedBy orgism:;
skos:definition """Specifying the first grade descendant of an organism or group of organisms."""@en;
rdfs:subPropertyOf agent:hasChild;
rdfs:domain [
owl:unionOf(orgism:BiologicalParent orgism:BiologicalParents)
];
rdfs:range orgism:BiologicalChild.
orgism:taxon
a owl:ObjectProperty;
rdfs:isDefinedBy orgism:;
skos:definition """Specifying the taxonomic identity of an organism as defined in uniprot taxonomy."""@en;
rdfs:domain orgism:Organism;
rdfs:range unicore:Taxon. # conflict: uniprot considers a taxon same as an organism, cf. ObjectProperty :organism
#orgism:taxonRank # provided by unicore:
# skos:definition """Specifying the taxonomic rank of an organism."""@en;
# rdfs:subPropertyOf fos:quality;
# rdfs:domain orgism:Taxon;
# rdfs:range [owl:oneOf(orgism:Domain orgism:Kingdom orgism:Subkingdom orgism:Phylum orgism:Subphylum orgism:Class orgism:Subclass orgism:Order orgism:Superfamily orgism:Family orgism:Subfamily orgism:Tribe orgism:Subtribe orgism:Genus orgism:Species orgism:Subspecies)].
#orgism:taxonName # provided by unicore:
# skos:definition """Specifying the taxonomic name of an organism."""@en;
# rdfs:subPropertyOf foaf:name;
# rdfs:domain orgism:Taxon;
# rdfs:range rdfs:Literal.