#
# Prefixes
#

@prefix dce: <http://purl.org/dc/elements/1.1/>.
@prefix dct: <http://purl.org/dc/terms/>.
@prefix foaf: <http://xmlns.com/foaf/0.1/>.
@prefix owl: <http://www.w3.org/2002/07/owl#>.
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.
@prefix skos: <http://www.w3.org/2004/02/skos/core#>.
@prefix unicore: <http://purl.uniprot.org/core/>.
@prefix xsd: <http://www.w3.org/2001/XMLSchema#>.
@prefix snomedct: <http://www.ihtsdo.org/>.
@prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#>.

@prefix agent: <http://eulersharp.sourceforge.net/2003/03swap/agent#>.
@prefix event: <http://eulersharp.sourceforge.net/2003/03swap/event#>.
@prefix fos: <http://eulersharp.sourceforge.net/2003/03swap/foster#>.

@prefix clinskosch: <http://www.agfa.com/w3c/2009/clinicalSKOSSchemes#>.

@prefix organism: <http://eulersharp.sourceforge.net/2003/03swap/organism#>.

organism:
	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 """organism"""@en;
	dce:language """English"""@en.

#
# Classes
#

organism:Organism
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:label """organism"""@en;
	skos:definition """Something that lives."""@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, geo:SpatialThing, [
		a owl:Restriction;
		owl:onProperty organism:beingState;
		owl:hasValue organism:alive];
	owl:disjointWith unicore:Taxon;
	skos:exactMatch [
		a skos:Concept;
		skos:inScheme clinskosch:sct20080731;
		skos:notation "410607006"^^clinskosch:sct20080731DT].

organism:Life
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:label """life"""@en;
	skos:definition """The process of being alive."""@en;
	rdfs:subClassOf event:Process, event:Existence.

organism:alive
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:label """alive"""@en;
	skos:definition """State of being alive."""@en;
	skos:note """Up till now no satisfying definition."""@en.

organism:dead
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	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:sct20080731DT
	];
	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
	].

organism:IndividualLife
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:label """individual life"""@en;
	skos:definition """Life of an organism after birth."""@en;
	rdfs:subClassOf organism:Life.

#Following elements provided by http://purl.uniprot.org/core/
#organism:Taxon
#	a rdfs:Class;
#	rdfs:isDefinedBy organism:;
#	rdfs:label """taxonomic position"""@en;
#	skos:definition """Position of an organism in the hierarchy of the biological classification or taxonomy."""@en;
#	a rdfs:Class.
#organism:Domain down to organism:Subspecies rdfs:subClassOf organism:TaxonRank.

organism:DevelopmentState
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:label """development state"""@en;
	skos:definition """Any state of development."""@en.

organism:immature
	rdfs:isDefinedBy organism:;
	rdfs:label """immature"""@en;
	skos:definition """Property of being biologically not full-grown."""@en;
	a organism:DevelopmentState.

organism:mature
	rdfs:isDefinedBy organism:;
	rdfs:label """mature"""@en;
	skos:definition """Property of being biologically full-grown, capable of reproduction."""@en;
	a organism:DevelopmentState.

organism:MatureOrganism
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:label """mature organism"""@en;
	skos:definition """Organism being mature."""@en;
	rdfs:subClassOf organism:Organism;
	rdfs:subClassOf [
		a owl:Restriction;
		owl:onProperty organism:developmentState;
		owl:hasValue organism:mature
	].

organism:ImmatureOrganism
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:label """immature organism"""@en;
	skos:definition """Organism being immature."""@en;
	rdfs:subClassOf organism:Organism;
	rdfs:subClassOf [
		a owl:Restriction;
		owl:onProperty organism:developmentState;
		owl:hasValue organism:immature
	].

organism:PregnantOrganism
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:label """pregnant organism"""@en;
	skos:definition """Organism being pregnant."""@en;
	rdfs:subClassOf organism:Organism;
	rdfs:subClassOf [
		a owl:Restriction;
		owl:onProperty organism:gravidity;
		owl:someValuesFrom organism:pregnant
	].

organism:Gravidity
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:label """gravidity"""@en;
	skos:definition """Any state of gravidity."""@en;
	owl:oneOf (organism:pregnant organism:nonpregnant).

organism:pregnant
	rdfs:isDefinedBy organism:;
	rdfs:label """pregnant"""@en;
	skos:definition """State of an organism of having offspring developing in its body."""@en;
	a organism:Gravidity.

organism:nonpregnant
	rdfs:isDefinedBy organism:;
	rdfs:label """nonpregnant"""@en;
	skos:definition """State of an organism of not having offspring developing in its body."""@en;
	a organism:Gravidity.
	
organism:BiologicalParent
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:label """biological parent"""@en;
	skos:definition """First grade ascendant of an organism."""@en;
	rdfs:subClassOf agent:Parent, organism:MatureOrganism;
	rdfs:comment """Organism that produces another."""@en.

organism:BiologicalAncestry
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:subClassOf agent:Ancestry;
	rdfs:subClassOf [
		a owl:Restriction;
		owl:onProperty foaf:member;
		owl:someValuesFrom organism:BiologicalParent
	].

organism:BiologicalParents
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:subClassOf organism:BiologicalAncestry.
	# restriction: all parents need to have a same biological child

organism:BiologicalMother
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:label """biological mother"""@en;
	skos:definition """Female biological parent."""@en;
	rdfs:subClassOf organism:BiologicalParent;
	owl:disjointWith organism:BiologicalFather.

organism:BiologicalFather
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:label """biological father"""@en;
	skos:definition """Male biological parent."""@en;
	rdfs:subClassOf organism:BiologicalParent.
	
organism:BiologicalChild
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:label """biological child"""@en;
	skos:definition """First grade living descendant of any kind."""@en;
	rdfs:subClassOf agent:Child, organism:Organism;
	rdfs:comment """Organism that is produced by another."""@en;
	rdfs:subClassOf [
		a owl:Restriction;
		owl:onProperty organism:hasBiologicalParent;
		owl:minCardinality "1"^^xsd:nonNegativeInteger
	];
	skos:exactMatch [
		a skos:Concept;
		skos:inScheme clinskosch:sct20080731;
		skos:notation "75226009"^^clinskosch:sct20080731DT
	].

organism:BiologicalOffspring
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:label """biological offspring"""@en;
	rdfs:subClassOf agent:Offspring;
	rdfs:subClassOf [
		a owl:Restriction;
		owl:onProperty foaf:member;
		owl:allValuesFrom agent:BiologicalDescendant
	].

organism:BiologicalChildren
	a rdfs:Class;
	rdfs:isDefinedBy organism:;
	rdfs:subClassOf organism:BiologicalOffspring;
	rdfs:subClassOf [
		a owl:Restriction;
		owl:onProperty foaf:member;
		owl:allValuesFrom organism:BiologicalChild
	].
	# restriction: all children need to have a same biological parent

#
# Properties
#

organism:beingState
	a owl:ObjectProperty;
	rdfs:isDefinedBy organism:;
	skos:definition """Specifying a state of being of something."""@en;
	rdfs:range [owl:oneOf(organism:alive organism:dead)].

organism:lives
	a owl:ObjectProperty;
	rdfs:isDefinedBy organism:;
	skos:definition """Specifying a life process of an organism."""@en;
	rdfs:subPropertyOf event:exists;
	rdfs:domain organism:Organism;
	rdfs:range organism:Life.

organism:developmentState
	a owl:ObjectProperty;
	rdfs:isDefinedBy organism:;
	skos:definition """Specifying the state of development of an individual organism."""@en;
	rdfs:domain organism:Organism;
	rdfs:range organism:DevelopmentState.

organism:gravidity
	a owl:ObjectProperty;
	rdfs:isDefinedBy organism:;
	skos:definition """Specifying the gravidity of an organism."""@en;
	rdfs:domain organism:Organism;
	rdfs:range organism:Gravidity.

organism:begins
	a owl:DatatypeProperty;
	rdfs:isDefinedBy organism:;
#	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 organism:IndividualLife;
	rdfs:range xsd:dateTime;
	skos:exactMatch [
		a skos:Concept;
		skos:inScheme clinskosch:sct20080731;
		skos:notation "184099003"^^clinskosch:sct20080731DT
	].

#organism:birthTime
#	a owl:DatatypeProperty;
#	rdfs:isDefinedBy organism:;
#	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 organism:birthDate.

organism:birthDate
	a owl:DatatypeProperty;
	rdfs:isDefinedBy organism:;
	skos:definition """Specifying a snapshot an organism is born."""@en;
	owl:propertyChainAxiom (organism:lives organism:begins); # -> owl:objectPropertyChain?
	rdfs:domain organism:Organism;
	rdfs:range xsd:dateTime.

organism:ends
	a owl:DatatypeProperty;
	rdfs:isDefinedBy organism:;
#	rdfs:label """died"""@en;
	skos:definition """Specifying the end of a life of an organism."""@en;
	rdfs:subPropertyOf event:expires;
	rdfs:domain organism:Life;
	rdfs:range xsd:dateTime;
	skos:exactMatch [
		a skos:Concept;
		skos:inScheme clinskosch:sct20080731;
		skos:notation "399753006"^^clinskosch:sct20080731DT
	].
	
#organism:deathTime
#	a owl:DatatypeProperty;
#	rdfs:isDefinedBy organism:;
#	rdfs:label """death time"""@en;
#	skos:definition """Specifying the time of ceasing to be an organism."""@en;
#	rdfs:subPropertyOf organism:deathDate.

organism:deathDate
	a owl:DatatypeProperty;
	rdfs:isDefinedBy organism:;
	skos:definition """Specifying a snapshot an organism died."""@en;
	owl:propertyChainAxiom (organism:lives organism:ends);
	rdfs:domain organism:Organism;
	rdfs:range xsd:dateTime.

organism:hasBiologicalParent
	a owl:ObjectProperty;
	rdfs:isDefinedBy organism:;
	skos:definition """Specifying the first grade ascendent of an organism or group of organisms."""@en;
	rdfs:subPropertyOf agent:hasParent;
	rdfs:domain [
		owl:unionOf(organism:BiologicalChild organism:BiologicalChildren)
	];
	rdfs:range organism:BiologicalParent.
	
organism:biologicalMother
	a owl:ObjectProperty, owl:FunctionalProperty;
	rdfs:isDefinedBy organism:;
	skos:definition """Specifying the first grade female ascendent of an organism."""@en;
	rdfs:subPropertyOf organism:hasBiologicalParent;
	rdfs:domain organism:BiologicalChild;
	rdfs:range organism:BiologicalMother.
	
organism:biologicalFather
	a owl:ObjectProperty, owl:FunctionalProperty;
	rdfs:isDefinedBy organism:;
	skos:definition """Specifying the first grade male ascendent of an organism."""@en;
	rdfs:subPropertyOf organism:hasBiologicalParent;
	rdfs:domain organism:BiologicalChild;
	rdfs:range organism:BiologicalFather.

organism:hasBiologicalChild
	a owl:ObjectProperty;
	rdfs:isDefinedBy organism:;
	skos:definition """Specifying the first grade descendant of an organism or group of organisms."""@en;
	rdfs:subPropertyOf agent:hasChild;
	rdfs:domain [
		owl:unionOf(organism:BiologicalParent organism:BiologicalParents)
	];
	rdfs:range organism:BiologicalChild.

organism:taxon
	a owl:ObjectProperty;
	rdfs:isDefinedBy organism:;
	skos:definition """Specifying the taxonomic identity of an organism as defined in uniprot taxonomy."""@en;
	rdfs:domain organism:Organism;
	rdfs:range unicore:Taxon. # conflict: uniprot considers a taxon same as an organism, cf. ObjectProperty :organism

#organism:taxonRank # provided by unicore:
#	skos:definition """Specifying the taxonomic rank of an organism."""@en;
#	rdfs:subPropertyOf fos:quality;
#	rdfs:domain organism:Taxon;
#	rdfs:range [owl:oneOf(organism:Domain organism:Kingdom organism:Subkingdom organism:Phylum organism:Subphylum organism:Class organism:Subclass organism:Order organism:Superfamily organism:Family organism:Subfamily organism:Tribe organism:Subtribe organism:Genus organism:Species organism:Subspecies)].

#organism:taxonName # provided by unicore:
#	skos:definition """Specifying the taxonomic name of an organism."""@en;
#	rdfs:subPropertyOf foaf:name;
#	rdfs:domain organism:Taxon;
#	rdfs:range rdfs:Literal.