pco-base.obo

format-version: 1.2
data-version: pco/releases/2021-05-03/pco-base.owl
remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators.
ontology: pco/pco-base
property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0001-8815-0078 xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "David Osumi-Sutherland" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "Jie Zheng" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "Pier Luigi Buttigieg" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "Ramona Walls" xsd:string
property_value: http://purl.org/dc/elements/1.1/description "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology." xsd:string
property_value: http://purl.org/dc/elements/1.1/title "Population and Community Ontology" xsd:string
property_value: http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 xsd:string
property_value: http://purl.org/dc/terms/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string

[Term]
id: CARO:0000012
name: multicellular organism
def: "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." []
comment: MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history.
comment: MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities.
is_a: CARO:0010004 ! organism
property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string
property_value: IAO:0000589 "multicellular organism" xsd:string

[Term]
id: CARO:0001010
name: organism or virus or viroid
def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." []
is_a: BFO:0000040
property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string
property_value: IAO:0000589 "organism or virus" xsd:string

[Term]
id: CARO:0010004
name: organism
def: "An individual member of a clade." []
comment: A general term for organism that is agnostic about single cell vs multi-cellular.  Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure.  So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms.
is_a: CARO:0001010 ! organism or virus or viroid
property_value: http://purl.obolibrary.org/obo/IAO_created_by "mah" xsd:string
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string
property_value: IAO:0000589 "organism" xsd:string

[Term]
id: ECOCORE:00000045
is_a: CARO:0001010 ! organism or virus or viroid

[Term]
id: GO:0051704
is_a: BFO:0000015

[Term]
id: IAO:0000030
is_a: BFO:0000031

[Term]
id: PCO:0000000
name: collection of organisms
def: "A material entity that consists of two or more organisms, viruses, or viroids." []
comment: May be of the same or different species.
intersection_of: BFO:0000027
intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid
intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid
relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid
property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000118 "group of organism" xsd:string
property_value: IAO:0000118 "organism collection" xsd:string

[Term]
id: PCO:0000001
name: population of organisms
def: "A collection of organisms, all of the same species, that live in the same place." []
comment: It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. \n\nClasses for population already  exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used.
is_a: PCO:0000018 ! single-species collection of organisms
property_value: IAO:0000112 "" xsd:string
property_value: IAO:0000112 "This a general term that can include every organism of a species living in an area or any subset of them.  Subclasses can be more specific as needed." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000119 ISBN:0878932739 xsd:string

[Term]
id: PCO:0000002
name: ecological community
def: "A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members." []
comment: 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.
is_a: PCO:0000029 ! multi-species collection of organisms
property_value: IAO:0000118 "multispecies community" xsd:string
property_value: IAO:0000119 ISBN:0865423504 xsd:string

[Term]
id: PCO:0000003
name: quality of a population
def: "A quality that inheres in a population of organisms." []
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.
intersection_of: PATO:0002003
intersection_of: RO:0000052 PCO:0000001 ! population of organisms
property_value: IAO:0000114 IAO:0000428
property_value: 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." xsd:string
property_value: IAO:0000116 "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." xsd:string

[Term]
id: PCO:0000004
name: quality of an ecological community
def: "A quality that inheres in a community." []
comment: Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual.
intersection_of: PATO:0002003
intersection_of: RO:0000052 PCO:0000002 ! ecological community
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000116 "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string

[Term]
id: PCO:0000005
name: population process
def: "A process that has as primary participant a population. Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction." []
comment: The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes.
is_a: BFO:0000015
relationship: RO:0000057 PCO:0000001 ! population of organisms
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000006
name: population birth rate
def: "The rate of birth of a population of organisms." []
is_a: PATO:0000161
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000007
name: population death rate
def: "The rate of death of a population of organsisms." []
is_a: PATO:0000161
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000008
name: population growth rate
def: "The rate of growth of a population." []
is_a: PATO:0000161
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000009
name: obsolete carrying capacity
def: "The maximum number of individuals that can be supported in  a population that is growing according to logistic growth." []
is_a: ObsoleteClass
property_value: IAO:0000116 "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string
property_value: IAO:0000119 ISBN:0878932739 xsd:string
property_value: IAO:0000231 IAO:0000423
is_obsolete: true

[Term]
id: PCO:0000010
name: community species richness
def: "The number of different species represented in an ecological community." []
is_a: PCO:0000004 ! quality of an ecological community
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000116 "This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019)." xsd:string
property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_richness" xsd:string

[Term]
id: PCO:0000011
name: population growth
def: "A process that leads to a change in the number of individuals (positive or negative) in a population." []
is_a: PCO:0000005 ! population process
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000012
name: logistic population growth
def: "A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat." []
is_a: PCO:0000011 ! population growth
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000013
name: exponential population growth
def: "A population growth process that leads to an exponential increase in the number of individuals in a population." []
is_a: PCO:0000011 ! population growth
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000014
name: obsolete predator role
is_a: ObsoleteClass
property_value: IAO:0000116 "Interactions are now covered in EcoCore ontology." xsd:string
is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"}

[Term]
id: PCO:0000015
name: obsolete prey role
is_a: ObsoleteClass
property_value: IAO:0000116 "Interactions are now covered in EcoCore ontology." xsd:string
is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"}

[Term]
id: PCO:0000016
name: obsolete symbiont role
is_a: ObsoleteClass
property_value: IAO:0000116 "Interactions are now covered in EcoCore ontology." xsd:string
is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"}

[Term]
id: PCO:0000017
name: species as a collection of organisms
def: "A collection of organisms that has as members every organism of given species and no organisms of any other species." []
def: "A collection of organisms that has as parts every organism of a species and no organisms of any other species." []
comment: This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user.
synonym: "taxonomic group" EXACT []
xref: GENO:0000113
xref: Species
xref: TAXRANK:0000006
is_a: PCO:0000018 ! single-species collection of organisms
is_a: PCO:0000059 ! taxon as collection of organisms
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000116 "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string

[Term]
id: PCO:0000018
name: single-species collection of organisms
def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." []
is_a: PCO:0000000 ! collection of organisms
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000118 "collection of organisms of the same species" xsd:string

[Term]
id: PCO:0000019
name: community species diversity
def: "The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness." []
comment: The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified.
is_a: PCO:0000004 ! quality of an ecological community
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000116 "If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity." xsd:string
property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_diversity" xsd:string

[Term]
id: PCO:0000020
name: family
def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." []
comment: Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry.
is_a: PCO:0000018 ! single-species collection of organisms
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "Needs axioms for family relationships." xsd:string
property_value: IAO:0000119 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 xsd:string

[Term]
id: PCO:0000021
name: population extinction
def: "A population process that ultimately leads to the death of all individuals in a population." []
is_a: PCO:0000005 ! population process
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000022
name: species extinction
def: "A process that ultimately leads to the death of all individuals in a population." []
is_a: BFO:0000015
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000023
name: community species evenness
def: "A quality of an ecological community that reflects how close in abundance all species in a community are." []
is_a: PCO:0000004 ! quality of an ecological community
property_value: 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." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_evenness" xsd:string

[Term]
id: PCO:0000024
name: household
def: "An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people." []
is_a: PCO:0000031 ! organismal entity
relationship: RO:0002321 ENVO:01000744
relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"}
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 https://orcid.org/0000-0002-2999-0103
property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:string

[Term]
id: PCO:0000025
name: obsolete red population
comment: This is an example population added to demonstrate the modeling pattern for collections of organisms.
is_a: ObsoleteClass
property_value: IAO:0000231 IAO:0000002
is_obsolete: true

[Term]
id: PCO:0000026
name: obsolete red organism
comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query.
is_a: ObsoleteClass
property_value: IAO:0000231 IAO:0000002
is_obsolete: true

[Term]
id: PCO:0000027
name: collection of humans
def: "A collection of organisms of the same species that has as members only humans." []
is_a: PCO:0000018 ! single-species collection of organisms
intersection_of: PCO:0000018 ! single-species collection of organisms
intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"}
intersection_of: RO:0002351 NCBITaxon:9606 {minCardinality="2"}
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000118 "human community" xsd:string
property_value: IAO:0000118 "human population" xsd:string

[Term]
id: PCO:0000028
name: obsolete community
def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." []
comment: 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).
is_a: ObsoleteClass
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: PCO:0000029
name: multi-species collection of organisms
def: "A collection of organisms that consists of two or more organisms from at least two species." []
is_a: PCO:0000000 ! collection of organisms
relationship: RO:0002351 PCO:0000001 {minCardinality="2"} ! population of organisms
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string

[Term]
id: PCO:0000030
name: agricultural household
name: obsolete organismal entity
def: "A household in which the majority of the income of its members is derived from agricultural activities." []
def: "A material entity that is one or more organisms, viruses or viroids." []
is_a: ObsoleteClass
is_a: PCO:0000024 ! household
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string
property_value: IAO:0000231 "wrong IRI form" xsd:string
is_obsolete: true
replaced_by: http://purl.obolibrary.org/obo/PCO_0000031

[Term]
id: PCO:0000031
name: organismal entity
def: "A material entity that is one or more organisms, viruses or viroids." []
is_a: BFO:0000040
union_of: CARO:0001010 ! organism or virus or viroid
union_of: PCO:0000000 ! collection of organisms
property_value: IAO:0000114 IAO:0000120

[Term]
id: PCO:0000032
name: biological family
def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." []
is_a: PCO:0000020 ! family
property_value: IAO:0000118 "genealogical family" xsd:string
property_value: IAO:0000119 "Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/" xsd:string

[Term]
id: PCO:0000033
name: human social gathering activity
def: "A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially." []
is_a: GO:0035176
relationship: RO:0000057 PCO:0000027 ! collection of humans
property_value: IAO:0000116 "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029" xsd:string
property_value: IAO:0000119 "GenEpiO curators" xsd:string

[Term]
id: PCO:0000034
name: human community event
def: "A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area." []
is_a: PCO:0000033 ! human social gathering activity
property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034" xsd:string
property_value: IAO:0000119 "GenEpio curators" xsd:string

[Term]
id: PCO:0000035
name: party
def: "A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose." []
is_a: PCO:0000033 ! human social gathering activity
property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030" xsd:string
property_value: IAO:0000119 "GenEpiO curators" xsd:string

[Term]
id: PCO:0000037
name: potluck
def: "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." []
is_a: PCO:0000033 ! human social gathering activity
property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string
property_value: IAO:0000119 "GenEpio curators" xsd:string

[Term]
id: PCO:0000038
name: wedding
def: "A human social gathering at which two people are married. May include a legal or social ceremony." []
is_a: PCO:0000033 ! human social gathering activity
property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031" xsd:string
property_value: IAO:0000119 "GenEpio curators" xsd:string

[Term]
id: PCO:0000039
name: baby shower
def: "A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby." []
is_a: PCO:0000033 ! human social gathering activity
property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032" xsd:string
property_value: IAO:0000119 "GenEpiO curators" xsd:string

[Term]
id: PCO:0000040
name: obsolete tidal mangrove shrubland community
def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." []
synonym: "mangrove community" RELATED []
synonym: "tidal shrubland community" RELATED []
xref: https://cmecscatalog.org/cmecs/classification/unit/577.html
is_a: ObsoleteClass
property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: PCO:0000041
name: obsolete invisible to unaided eye
def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." []
comment: should move to PATO
is_a: ObsoleteClass
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: PCO:0000042
name: obsolete microbe
synonym: "microbial organism" EXACT []
is_a: ObsoleteClass
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: PCO:0000043
name: obsolete collection of microbial organisms
def: "A collection of organisms consisting of two or more microbes." []
is_a: ObsoleteClass
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: PCO:0000044
name: obsolete multi-species collection of microbes
def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." []
is_a: ObsoleteClass
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: PCO:0000045
name: obsolete single species collection of microbes
def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." []
is_a: ObsoleteClass
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: PCO:0000046
name: obsolete microbial population
def: "A population of organisms consisting of only microbes of the same species, that live in the same place." []
synonym: "microbiota" BROAD []
is_a: ObsoleteClass
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: PCO:0000047
name: tidal mangrove shrubland community
def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." []
synonym: "mangrove community" RELATED []
synonym: "tidal shrubland community" RELATED []
xref: https://cmecscatalog.org/cmecs/classification/unit/577.html
is_a: PCO:0000002 ! ecological community
relationship: BFO:0000050 ENVO:01001369
property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string

[Term]
id: PCO:0000048
name: invisible to unaided eye
def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." []
comment: should move to PATO
is_a: PATO:0001241

[Term]
id: PCO:0000049
name: microbe
synonym: "microbial organism" EXACT []
is_a: CARO:0001010 ! organism or virus or viroid

[Term]
id: PCO:0000050
name: collection of microbial organisms
def: "A collection of organisms consisting of two or more microbes." []
intersection_of: RO:0002351 PCO:0000049 {all_only="true"} ! microbe
intersection_of: RO:0002351 PCO:0000049 {minCardinality="2"} ! microbe
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string

[Term]
id: PCO:0000051
name: multi-species collection of microbes
def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." []
is_a: PCO:0000029 ! multi-species collection of organisms
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string

[Term]
id: PCO:0000052
name: single species collection of microbes
def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." []
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string

[Term]
id: PCO:0000053
name: microbial population
def: "A population of organisms consisting of only microbes of the same species, that live in the same place." []
synonym: "microbiota" BROAD []
is_a: PCO:0000001 ! population of organisms
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string

[Term]
id: PCO:0000054
name: number of generations of multicellular organism
def: "A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism." [] {comment="NCIT:C88214", comment="EFO:0000507"}
synonym: "number of generations" BROAD []
is_a: STATO:0000047
relationship: IAO:0000136 CARO:0000012 ! multicellular organism
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-2999-0103

[Term]
id: PCO:0000057
name: overcrowded population
def: "An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels." []
synonym: "increased density of population" EXACT []
is_a: PCO:0000003 ! quality of a population
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0000058
name: overcrowded human population
def: "A quality of a human population such that the density humans in an area is increased beyond sustainable levels." []
is_a: PCO:0000057 ! overcrowded population
intersection_of: PCO:0000057 ! overcrowded population
intersection_of: RO:0000052 PCO:0000027 ! collection of humans
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0000059
name: taxon as collection of organisms
def: "A collection of organisms that has as members every organism of a taxon and no organisms of any other equal or higher ranked taxon. The taxon may be at any level. If the taxon is species, then this is the same as the class species as a collection of organisms. When defining a taxon, it is generally understood that members include both living organisms and dead organisms that are known through specimens or observations." []
comment: This term is neutral with respect to which organisms are included in a taxon. Membership will depend on the taxon concept and the assertions used to define the taxon. These criteria must be specified by the user. The best practice is to refer to a formal taxon description, rather than informal names "Genus species" without an authority.
xref: data:1868
is_a: PCO:0000000 ! collection of organisms
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0000060
name: microbial parasite
def: "An organism or virus or viroid that is a microbe and a parasite." []
is_a: ECOCORE:00000146
is_a: PCO:0000049 ! microbe
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0000061
name: parasite isolate population
def: "A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations." []
is_a: PCO:0000053 ! microbial population
relationship: RO:0002351 PCO:0000060 ! microbial parasite
property_value: IAO:0000112 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811772/
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078
property_value: IAO:0000117 "VEuPathDB" xsd:string

[Term]
id: PCO:0000062
name: Shannon diversity index
def: "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)." []
synonym: "Shannon entropy" EXACT []
synonym: "Shannon's diversity index" EXACT []
synonym: "Shannon-Wiener index" EXACT []
is_a: PCO:0000019 ! community species diversity
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/shannonDI.html
property_value: IAO:0000119 "Shannon_index"

[Term]
id: PCO:0000063
name: Simpson diversity index
def: "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)." []
synonym: "Simpson index" EXACT []
is_a: PCO:0000019 ! community species diversity
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html
property_value: IAO:0000119 "Simpson_index"

[Term]
id: PCO:0000064
name: inverse Simpson diversity index
def: "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)." []
is_a: PCO:0000019 ! community species diversity
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html
property_value: IAO:0000119 "Inverse_Simpson_index"

[Term]
id: PCO:0000073
name: alga excluding Cyanobacteria
def: "An organism that is part of a polyphyletic group of mostly photosynthetic Eukaryotes  encompassing green plants excluding Embriophyta (land plants). Included organisms range from unicellular microalgae, such as Chlorella and diatoms to multicellular forms such as giant kelp." []
synonym: "alga" EXACT []
synonym: "algae" EXACT []
synonym: "seaweed" NARROW []
is_a: CARO:0010004 ! organism
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Algae

[Term]
id: PCO:0000074
name: alpha diversity
def: "A community species diversity that is the mean species diversity at a site or within a specific habitat." []
synonym: "α-diversity" EXACT []
is_a: PCO:0000019 ! community species diversity
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078
property_value: IAO:0000119 Alpha:diversity

[Term]
id: PCO:0000075
name: beta diversity
def: "A community species diversity that is the ratio between regional and local species diversity." []
synonym: "true beta diversity" EXACT []
synonym: "β-diversity" EXACT []
is_a: PCO:0000019 ! community species diversity
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078
property_value: IAO:0000119 Beta:diversity

[Term]
id: PCO:0000076
name: gamma diversity
def: "A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity." []
synonym: "γ-diversity" EXACT []
is_a: PCO:0000019 ! community species diversity
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078
property_value: IAO:0000119 Gamma:diversity

[Term]
id: PCO:0000077
name: plant density
is_a: PATO:0001019
property_value: IAO:0000116 "TBD: add logical definition" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078
property_value: IAO:0000117 "The density of plants in an ecological community or population, often measured as the number of plants per area." xsd:string

[Term]
id: PCO:0000078
name: seedling density
def: "The density of seedlings in an ecological community or population, often measured as the number of seedlings per area." []
is_a: PCO:0000077 ! plant density
property_value: IAO:0000116 "TBD: add logical definition" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0000079
name: plant density of a population
def: "The density of plants in a population or organisms (a single species), often measured as the number of plants per area." []
is_a: PCO:0000003 ! quality of a population
is_a: PCO:0000077 ! plant density
property_value: IAO:0000116 "TBD: add logical definition" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0000080
name: plant density of an ecological community
def: "The density of plants in an ecological community (multiple species), often measured as the number of plants per area." []
is_a: PCO:0000004 ! quality of an ecological community
is_a: PCO:0000077 ! plant density
property_value: IAO:0000116 "TBD: add logical definition" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0000081
name: seedling density of a population
def: "The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area." []
is_a: PCO:0000003 ! quality of a population
is_a: PCO:0000078 ! seedling density
property_value: IAO:0000116 "TBD: add logical definition" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0000082
name: seedling density of an ecological community
def: "The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area." []
is_a: PCO:0000004 ! quality of an ecological community
is_a: PCO:0000078 ! seedling density
property_value: IAO:0000116 "TBD: add logical definition" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0001000
name: pair of interacting organisms
def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." []
intersection_of: PCO:0000000 ! collection of organisms
intersection_of: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid

[Term]
id: PCO:0001001
name: pair of interacting organisms of the same species
def: "A pair of interacting  organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other." []
is_a: PCO:0000018 ! single-species collection of organisms
is_a: PCO:0001000 ! pair of interacting organisms
property_value: IAO:0000114 IAO:0000428

[Term]
id: PCO:1000000
name: migratory population
def: "A population which is participating in a migration process." []
is_a: PCO:0000001 ! population of organisms
relationship: RO:0000056 PCO:1000001 ! population migration
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:1000001
name: population migration
def: "A population process during which a population moves from one area to another." []
comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations.
is_a: PCO:0000005 ! population process
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Migration xsd:string

[Term]
id: PCO:1000002
name: human population migration
def: "A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location." []
comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration
is_a: PCO:1000001 ! population migration
relationship: RO:0000057 PCO:0000027 ! collection of humans
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string

[Term]
id: PCO:1000003
name: human migratory population
def: "A migratory population of humans, travelling with the intention of settling in a new area." []
is_a: PCO:0000027 ! collection of humans
relationship: RO:0000056 PCO:1000002 ! human population migration
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string

[Term]
id: PCO:1000004
name: microbial community
def: "An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness." []
comment: The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another.
synonym: "microbiota" BROAD []
is_a: PCO:0000002 ! ecological community
is_a: PCO:0000051 ! multi-species collection of microbes
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string
property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 xsd:string
property_value: IAO:0000119 http://dx.doi.org/10.1038/ismej.2009.88 xsd:string

[Typedef]
id: PCO:0000055
name: obsolete has member of
property_value: IAO:0000231 IAO:0000103
is_obsolete: true