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add subclasses of community species diversity to fix #94
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@ramonawalls
ramonawalls committed Aug 20, 2020
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43 changes: 23 additions & 20 deletions src/ontology/catalog-v001.xml
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Expand Up @@ -11,25 +11,28 @@
<uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/iao/2019-08-26/ontology-metadata.owl" uri="http://purl.obolibrary.org/obo/iao/ontology-metadata.owl"/>
<uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/ro/releases/2019-09-25/ro.owl" uri="http://purl.obolibrary.org/obo/ro.owl"/>
<group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base="">
<uri id="Automatically generated entry, Timestamp=1597687302000" name="http://purl.obolibrary.org/obo/bfo.owl" uri="imports/input_files/bfo.owl"/>
<uri id="Automatically generated entry, Timestamp=1597687302000" name="http://purl.obolibrary.org/obo/envo.owl" uri="imports/input_files/envo.owl"/>
<uri id="Automatically generated entry, Timestamp=1597687302000" name="http://purl.obolibrary.org/obo/go.owl" uri="imports/input_files/go.owl"/>
<uri id="Automatically generated entry, Timestamp=1597687302000" name="http://purl.obolibrary.org/obo/ncbitaxon.owl" uri="imports/input_files/ncbitaxon.owl"/>
<uri id="Automatically generated entry, Timestamp=1597687302000" name="http://purl.obolibrary.org/obo/pato.owl" uri="imports/input_files/pato.owl"/>
<uri id="Automatically generated entry, Timestamp=1597687302000" name="http://purl.obolibrary.org/obo/pco.owl" uri="pco.owl"/>
<uri id="Automatically generated entry, Timestamp=1597687302000" name="http://purl.obolibrary.org/obo/pco/imports/bfo_import.owl" uri="imports/bfo_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1597687302000" name="http://purl.obolibrary.org/obo/pco/imports/envo_import.owl" uri="imports/envo_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1597687302000" name="http://purl.obolibrary.org/obo/pco/imports/go_import.owl" uri="imports/go_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1597687302000" name="http://purl.obolibrary.org/obo/pco/imports/ncbitaxon_import.owl" uri="imports/ncbitaxon_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1597687302000" name="http://purl.obolibrary.org/obo/pco/imports/pato_import.owl" uri="imports/pato_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1597687302000" name="http://purl.obolibrary.org/obo/pco/imports/ro_import.owl" uri="imports/ro_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1597687302000" name="http://purl.obolibrary.org/obo/pco/imports/stato_import.owl" uri="imports/stato_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1597687302000" name="http://purl.obolibrary.org/obo/pco/pco-base.owl" uri="pco-base.owl"/>
<uri id="Automatically generated entry, Timestamp=1597687302000" name="http://purl.obolibrary.org/obo/pco/pco-full.owl" uri="pco-full.owl"/>
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<uri id="Automatically generated entry, Timestamp=1597687302000" name="duplicate:http://purl.obolibrary.org/obo/stato.owl" uri="imports/input_files/stato.owl.xml"/>
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<uri id="Automatically generated entry, Timestamp=1597941116471" name="http://purl.obolibrary.org/obo/bfo.owl" uri="imports/input_files/bfo.owl"/>
<uri id="Automatically generated entry, Timestamp=1597941116471" name="http://purl.obolibrary.org/obo/ecocore.owl" uri="imports/input_files/ecocore.owl"/>
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<uri id="Automatically generated entry, Timestamp=1597941116471" name="http://purl.obolibrary.org/obo/ncbitaxon.owl" uri="imports/input_files/ncbitaxon.owl"/>
<uri id="Automatically generated entry, Timestamp=1597941116471" name="http://purl.obolibrary.org/obo/pato.owl" uri="imports/input_files/pato.owl"/>
<uri id="Automatically generated entry, Timestamp=1597941116471" name="http://purl.obolibrary.org/obo/pco.owl" uri="pco.owl"/>
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<uri id="Automatically generated entry, Timestamp=1597941116471" name="http://purl.obolibrary.org/obo/pco/imports/ecocore_import.owl" uri="imports/ecocore_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1597941116471" name="http://purl.obolibrary.org/obo/pco/imports/envo_import.owl" uri="imports/envo_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1597941116471" name="http://purl.obolibrary.org/obo/pco/imports/go_import.owl" uri="imports/go_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1597941116471" name="http://purl.obolibrary.org/obo/pco/imports/iao_import.owl" uri="imports/iao_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1597941116471" name="http://purl.obolibrary.org/obo/pco/imports/ncbitaxon_import.owl" uri="imports/ncbitaxon_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1597941116471" name="http://purl.obolibrary.org/obo/pco/imports/pato_import.owl" uri="imports/pato_import.owl"/>
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<uri id="Automatically generated entry, Timestamp=1597941116471" name="http://purl.obolibrary.org/obo/pco/pco-full.owl" uri="pco-full.owl"/>
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<uri id="Automatically generated entry, Timestamp=1597941116471" name="http://purl.obolibrary.org/obo/stato.owl" uri="imports/input_files/stato.owl"/>
<uri id="Automatically generated entry, Timestamp=1597941116471" name="shadowed:http://purl.obolibrary.org/obo/bfo.owl" uri="mirror/bfo.owl"/>
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</group>
</catalog>
41 changes: 38 additions & 3 deletions src/ontology/pco-edit.owl
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Expand Up @@ -253,8 +253,9 @@ obo:PCO_0000003 rdf:type owl:Class ;
rdf:type owl:Class
] ;
obo:IAO_0000114 obo:IAO_0000428 ;
obo:IAO_0000115 "A quality that inheres in a biological population."@en ;
obo:IAO_0000116 "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2."@en ;
obo:IAO_0000115 "A quality that inheres in a population of organisms."@en ;
obo:IAO_0000116 "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2."@en ,
"This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community." ;
rdfs:comment "Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term."@en ;
rdfs:label "quality of a population"@en .

Expand Down Expand Up @@ -491,7 +492,7 @@ obo:PCO_0000023 rdf:type owl:Class ;
rdfs:subClassOf obo:PCO_0000004 ;
obo:IAO_0000112 "If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even."@en ;
obo:IAO_0000114 obo:IAO_0000120 ;
obo:IAO_0000115 "A quality of a community that reflects how close in abundance all species in a community are."@en ;
obo:IAO_0000115 "A quality of an ecological community that reflects how close in abundance all species in a community are."@en ;
obo:IAO_0000119 "adapted from http://en.wikipedia.org/wiki/Species_evenness"@en ;
rdfs:label "community species evenness"@en .

Expand Down Expand Up @@ -864,6 +865,40 @@ obo:PCO_0000061 rdf:type owl:Class ;
rdfs:label "parasite isolate population"@en .


### http://purl.obolibrary.org/obo/PCO_0000062
obo:PCO_0000062 rdf:type owl:Class ;
rdfs:subClassOf obo:PCO_0000019 ;
obo:IAO_0000114 obo:IAO_0000125 ;
obo:IAO_0000115 "A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi)." ;
obo:IAO_0000119 <http://www.tiem.utk.edu/~gross/bioed/bealsmodules/shannonDI.html> ,
<https://en.wikipedia.org/wiki/Diversity_index#Shannon_index> ;
<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> "Shannon entropy" ,
"Shannon's diversity index" ,
"Shannon-Wiener index" ;
rdfs:label "Shannon diversity index"@en .


### http://purl.obolibrary.org/obo/PCO_0000063
obo:PCO_0000063 rdf:type owl:Class ;
rdfs:subClassOf obo:PCO_0000019 ;
obo:IAO_0000114 obo:IAO_0000125 ;
obo:IAO_0000115 "A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi)." ;
obo:IAO_0000119 <http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html> ,
<https://en.wikipedia.org/wiki/Diversity_index#Simpson_index> ;
<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> "Simpson index" ;
rdfs:label "Simpson diversity index"@en .


### http://purl.obolibrary.org/obo/PCO_0000064
obo:PCO_0000064 rdf:type owl:Class ;
rdfs:subClassOf obo:PCO_0000019 ;
obo:IAO_0000114 obo:IAO_0000125 ;
obo:IAO_0000115 "A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi)." ;
obo:IAO_0000119 <http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html> ,
<https://en.wikipedia.org/wiki/Diversity_index#Inverse_Simpson_index> ;
rdfs:label "inverse Simpson diversity index"@en .


### http://purl.obolibrary.org/obo/PCO_0001000
obo:PCO_0001000 rdf:type owl:Class ;
rdfs:subClassOf obo:BFO_0000040 ,
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