Revert "update definitions of ecological community, community"

This reverts commit 37f243c so we can do release.

Author: ramonawalls

src/ontology/pco.owl

@@ -98,14 +98,13 @@ Classes for population already  exist in IDO ('organism population', IDO_0000509
 AnnotationAssertion(obo:IAO_0000112 obo:PCO_0000001 ""@en)
 AnnotationAssertion(obo:IAO_0000114 obo:PCO_0000001 obo:IAO_0000125)
 SubClassOf(obo:PCO_0000001 obo:PCO_0000018)
+AnnotationAssertion(obo:IAO_0000114 obo:PCO_0000002 obo:IAO_0000125)
 AnnotationAssertion(obo:IAO_0000118 obo:PCO_0000002 "multispecies community"@en)
 AnnotationAssertion(obo:IAO_0000115 obo:PCO_0000002 "A community of at least two different species, living in a particular area. Must have at least two populations of different species as members."@en)
 AnnotationAssertion(rdfs:label obo:PCO_0000002 "ecological community"@en)
 AnnotationAssertion(obo:IAO_0000119 obo:PCO_0000002 "ISBN:0865423504")
-AnnotationAssertion(rdfs:comment obo:PCO_0000002 "Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community."@en)
-AnnotationAssertion(obo:IAO_0000114 obo:PCO_0000002 obo:IAO_0000123)
-AnnotationAssertion(obo:IAO_0000116 obo:PCO_0000002 "Not sure if the equivalancy axiom specifies that both populations are located in the same site.")
-EquivalentClasses(obo:PCO_0000002 ObjectIntersectionOf(ObjectMinCardinality(2 obo:RO_0002351 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:RO_0001025 obo:BFO_0000029) obo:PCO_0000001)) obo:PCO_0000028))
+AnnotationAssertion(rdfs:comment obo:PCO_0000002 "Ecological community is defined broadly here. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms."@en)
+EquivalentClasses(obo:PCO_0000002 ObjectIntersectionOf(ObjectMinCardinality(2 obo:RO_0002351 obo:PCO_0000001) obo:PCO_0000028))
 SubClassOf(obo:PCO_0000002 obo:PCO_0000029)
 AnnotationAssertion(rdfs:label obo:PCO_0000003 "quality of a population"@en)
 AnnotationAssertion(obo:IAO_0000115 obo:PCO_0000003 "A quality that inheres in a biological population."@en)
@@ -227,11 +226,11 @@ AnnotationAssertion(obo:IAO_0000118 obo:PCO_0000027 "human community"@en)
 AnnotationAssertion(obo:IAO_0000115 obo:PCO_0000027 "A collection of organisms of the same species that has as members only humans."^^xsd:string)
 AnnotationAssertion(rdfs:label obo:PCO_0000027 "collection of humans"@en)
 EquivalentClasses(obo:PCO_0000027 ObjectIntersectionOf(obo:PCO_0000018 ObjectAllValuesFrom(obo:RO_0002351 obo:NCBITaxon_9606) ObjectMinCardinality(2 obo:RO_0002351 obo:NCBITaxon_9606)))
-AnnotationAssertion(rdfs:comment obo:PCO_0000028 "These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a  human community, which is also a type of population) or a  or multi-species collection of organisms (as in an ecological community)."@en)
 AnnotationAssertion(rdfs:label obo:PCO_0000028 "community"@en)
 AnnotationAssertion(obo:IAO_0000114 obo:PCO_0000028 obo:IAO_0000123)
-AnnotationAssertion(obo:IAO_0000116 obo:PCO_0000028 "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete."@en)
+AnnotationAssertion(rdfs:comment obo:PCO_0000028 "These relations can include shared values, occupying the same spatial relation. A community be be a single species collection of organsisms (as in a  human community) or a  or multi-species collection of organisms (as in an ecological community)."@en)
 AnnotationAssertion(obo:IAO_0000115 obo:PCO_0000028 "A collection of organisms connected by social or biological relations (biotic interactions)."@en)
+AnnotationAssertion(obo:IAO_0000116 obo:PCO_0000028 "Need to specify axioms for the biological or social relations, once the relations are specified in the Relation Ontology."@en)
 SubClassOf(obo:PCO_0000028 ObjectIntersectionOf(ObjectMinCardinality(2 obo:RO_0002351 obo:CARO_0001010) ObjectAllValuesFrom(obo:RO_0002351 obo:CARO_0001010)))
 AnnotationAssertion(obo:IAO_0000116 obo:PCO_0000029 "Need to add axiom to specify that it has at a mimum members of two different species."@en)
 AnnotationAssertion(obo:IAO_0000114 obo:PCO_0000029 obo:IAO_0000123)
@@ -251,7 +250,5 @@ AnnotationAssertion(rdfs:label obo:PCO_0001001 "pair of interacting organisms of
 EquivalentClasses(obo:PCO_0001001 ObjectIntersectionOf(ObjectAllValuesFrom(obo:RO_0002351 ObjectExactCardinality(1 obo:RO_0002350 obo:PCO_0000017)) obo:PCO_0001000))
 AnnotationAssertion(rdfs:label pco:PCO_0000030 "organismal entity"@en)
 AnnotationAssertion(obo:IAO_0000115 pco:PCO_0000030 "A material entity that is one or more organisms, viruses or viroids.")
-AnnotationAssertion(obo:IAO_0000114 pco:PCO_0000030 obo:IAO_0000428)
-AnnotationAssertion(obo:IAO_0000116 pco:PCO_0000030 "Not sure if we need this union class.")
 EquivalentClasses(pco:PCO_0000030 ObjectUnionOf(obo:PCO_0000000 obo:CARO_0001010))
 )