From 08f374841d5fcf792285d43fc799a8cbb9b43066 Mon Sep 17 00:00:00 2001 From: RamonaWalls Date: Thu, 20 Aug 2020 09:44:49 -0700 Subject: [PATCH] add subclasses of community species diversity to fix #94 --- src/ontology/catalog-v001.xml | 43 +++++++++++++++++++---------------- src/ontology/pco-edit.owl | 41 ++++++++++++++++++++++++++++++--- 2 files changed, 61 insertions(+), 23 deletions(-) diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index 9cbacce..106713a 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -11,25 +11,28 @@ - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/pco-edit.owl b/src/ontology/pco-edit.owl index b218310..9c6c4ae 100644 --- a/src/ontology/pco-edit.owl +++ b/src/ontology/pco-edit.owl @@ -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 . @@ -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 . @@ -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 , + ; + "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 , + ; + "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 , + ; + 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 ,