Term IRI Term label Parent term IRI Parent term label Alternative term Definition http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module subset ontology An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. http://purl.obolibrary.org/obo/IAO_0000027 data item http://purl.obolibrary.org/obo/IAO_0000030 information content entity data a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. http://purl.obolibrary.org/obo/PCO_0000000 collection of organisms http://purl.obolibrary.org/obo/PCO_0000031 organismal entity organism collection A material entity that consists of two or more organisms, viruses, or viroids. http://purl.obolibrary.org/obo/PCO_0000002 ecological community http://purl.obolibrary.org/obo/PCO_0000029 multi-species collection of organisms multispecies community 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. http://purl.obolibrary.org/obo/PCO_0000018 single-species collection of organisms http://purl.obolibrary.org/obo/PCO_0000000 collection of organisms collection of organisms of the same species 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. http://purl.obolibrary.org/obo/PCO_0000027 collection of humans http://purl.obolibrary.org/obo/PCO_0000018 single-species collection of organisms human population A collection of organisms of the same species that has as members only humans. http://purl.obolibrary.org/obo/PCO_0000032 biological family http://purl.obolibrary.org/obo/PCO_0000020 family genealogical family A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. http://purl.obolibrary.org/obo/IAO_8000002 editors ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module source ontology module An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. http://purl.obolibrary.org/obo/IAO_8000005 import ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module import file A subset ontology module that is intended to be imported from another ontology. http://purl.obolibrary.org/obo/IAO_8000009 single layer subset ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module ribbon subset A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. http://purl.obolibrary.org/obo/IAO_8000010 exclusion subset ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module antislim A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. http://purl.obolibrary.org/obo/IAO_8000011 external import ontology module http://purl.obolibrary.org/obo/IAO_8000005 import ontology module external import An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. http://purl.obolibrary.org/obo/IAO_8000012 species subset ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module taxon subset A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. http://purl.obolibrary.org/obo/PCO_1000000 migratory population http://purl.obolibrary.org/obo/PCO_0000001 population of organisms A population which is participating in a migration process. http://purl.obolibrary.org/obo/PCO_1000001 population migration http://purl.obolibrary.org/obo/PCO_0000005 population process A population process during which a population moves from one area to another. http://purl.obolibrary.org/obo/PCO_1000002 human population migration http://purl.obolibrary.org/obo/PCO_1000001 population migration 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. http://purl.obolibrary.org/obo/PCO_1000003 human migratory population http://purl.obolibrary.org/obo/PCO_0000027 collection of humans A migratory population of humans, travelling with the intention of settling in a new area. http://purl.obolibrary.org/obo/PATO_0000001 quality http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities http://purl.obolibrary.org/obo/PATO_0000069 deviation (from_normal) http://purl.obolibrary.org/obo/PATO_0000068 qualitative A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. http://purl.obolibrary.org/obo/PATO_0000070 amount http://purl.obolibrary.org/obo/PATO_0000068 qualitative The number of entities of this type that are part of the whole organism. http://purl.obolibrary.org/obo/PATO_0000161 rate http://purl.obolibrary.org/obo/PATO_0002062 physical quality of a process A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. http://purl.obolibrary.org/obo/PATO_0000461 normal http://purl.obolibrary.org/obo/PATO_0000068 qualitative A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. http://purl.obolibrary.org/obo/PATO_0000467 present http://purl.obolibrary.org/obo/PATO_0000070 amount A quality inhering in a bearer by virtue of the bearer's existence. http://purl.obolibrary.org/obo/PATO_0000470 increased amount http://purl.obolibrary.org/obo/PATO_0002300 increased quality An amount which is relatively high. http://purl.obolibrary.org/obo/PATO_0000911 decreased rate http://purl.obolibrary.org/obo/PATO_0002302 decreased process quality A rate which is relatively low. http://purl.obolibrary.org/obo/PATO_0000912 increased rate http://purl.obolibrary.org/obo/PATO_0002304 increased process quality A rate which is relatively high. http://purl.obolibrary.org/obo/PATO_0001018 physical quality http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. http://purl.obolibrary.org/obo/PATO_0001019 mass density http://purl.obolibrary.org/obo/PATO_0001018 physical quality A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. http://purl.obolibrary.org/obo/PATO_0001164 dense http://purl.obolibrary.org/obo/PATO_0001019 mass density A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. http://purl.obolibrary.org/obo/PATO_0001236 process quality http://purl.obolibrary.org/obo/PATO_0000001 quality A quality which inheres in an process. http://purl.obolibrary.org/obo/PATO_0001241 physical object quality http://purl.obolibrary.org/obo/PATO_0000001 quality A quality which inheres in a continuant. http://purl.obolibrary.org/obo/PATO_0001415 morbidity http://purl.obolibrary.org/obo/PATO_0002003 population quality A quality inhering in a population by virtue of the proportion of its members that are ill at a given time. http://purl.obolibrary.org/obo/PATO_0001555 has number of http://purl.obolibrary.org/obo/PATO_0001241 physical object quality The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. http://purl.obolibrary.org/obo/PATO_0001788 increased mass density http://purl.obolibrary.org/obo/PATO_0002305 increased object quality A density which is higher relative to the normal or average. http://purl.obolibrary.org/obo/PATO_0001790 decreased mass density http://purl.obolibrary.org/obo/PATO_0002303 decreased object quality A density which is lower relative to the normal or average. http://purl.obolibrary.org/obo/PATO_0001997 decreased amount http://purl.obolibrary.org/obo/PATO_0002301 decreased quality An amount which is relatively low. http://purl.obolibrary.org/obo/PATO_0002003 population quality http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality that inheres in an entire population or part of a population. http://purl.obolibrary.org/obo/PATO_0002300 increased quality http://purl.obolibrary.org/obo/PATO_0000069 deviation (from_normal) A quality that has a value that is increased compared to normal or average. http://purl.obolibrary.org/obo/PATO_0002301 decreased quality http://purl.obolibrary.org/obo/PATO_0000069 deviation (from_normal) A quality that has a value that is decreased compared to normal or average. http://purl.obolibrary.org/obo/PATO_0002302 decreased process quality http://purl.obolibrary.org/obo/PATO_0002301 decreased quality A quality of a process that has a value that is decreased compared to normal or average. http://purl.obolibrary.org/obo/PATO_0002303 decreased object quality http://purl.obolibrary.org/obo/PATO_0002301 decreased quality A quality of an object that has a value that is decreased compared to normal or average. http://purl.obolibrary.org/obo/PATO_0002304 increased process quality http://purl.obolibrary.org/obo/PATO_0002300 increased quality A quality of a process that has a value that is increased compared to normal or average. http://purl.obolibrary.org/obo/PATO_0002305 increased object quality http://purl.obolibrary.org/obo/PATO_0002300 increased quality A quality of an object that has a value that is increased compared to normal or average. http://purl.obolibrary.org/obo/ECOCORE_00000146 parasite http://purl.obolibrary.org/obo/ECOCORE_00000045 symbiotroph A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host http://purl.obolibrary.org/obo/BFO_0000002 continuant http://purl.obolibrary.org/obo/BFO_0000001 entity An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000001 entity An entity that has temporal parts and that happens, unfolds or develops through time. http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. http://purl.obolibrary.org/obo/BFO_0000015 process http://purl.obolibrary.org/obo/BFO_0000003 occurrent An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. http://purl.obolibrary.org/obo/BFO_0000023 role http://purl.obolibrary.org/obo/BFO_0000017 realizable entity A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000004 independent continuant An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. http://purl.obolibrary.org/obo/IAO_0000078 curation status specification http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part http://purl.obolibrary.org/obo/IAO_0000027 data item Data about an ontology part is a data item about a part of an ontology, for example a term http://purl.obolibrary.org/obo/IAO_0000109 measurement datum http://purl.obolibrary.org/obo/IAO_0000027 data item A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. http://purl.obolibrary.org/obo/IAO_0000225 obsolescence reason specification http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. http://purl.obolibrary.org/obo/IAO_0000409 denotator type http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part A denotator type indicates how a term should be interpreted from an ontological perspective. http://purl.obolibrary.org/obo/PATO_0001338 mixed sex http://purl.obolibrary.org/obo/PATO_0002003 population quality A biological sex quality inhering in a population of multiple sexes. http://purl.obolibrary.org/obo/ECOCORE_00000045 symbiotroph http://purl.obolibrary.org/obo/CARO_0001010 organism or virus or viroid heterotroph that acquires nutrition from a symbiont http://purl.obolibrary.org/obo/STATO_0000047 count http://purl.obolibrary.org/obo/IAO_0000109 measurement datum a count is a data item denoted by an integer and represented the number of instances or occurences of an entity http://purl.obolibrary.org/obo/PCO_0000003 quality of a population http://purl.obolibrary.org/obo/PATO_0002003 population quality A quality that inheres in a population of organisms. http://purl.obolibrary.org/obo/PCO_0000004 quality of an ecological community http://purl.obolibrary.org/obo/PATO_0002003 population quality A quality that inheres in a community. http://purl.obolibrary.org/obo/PCO_0000005 population process http://purl.obolibrary.org/obo/BFO_0000015 process 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. http://purl.obolibrary.org/obo/PCO_0000006 population birth rate http://purl.obolibrary.org/obo/PATO_0000161 rate The rate of birth of a population of organisms. http://purl.obolibrary.org/obo/PCO_0000007 population death rate http://purl.obolibrary.org/obo/PATO_0000161 rate The rate of death of a population of organsisms. http://purl.obolibrary.org/obo/PCO_0000008 population growth rate http://purl.obolibrary.org/obo/PATO_0000161 rate The rate of growth of a population. http://purl.obolibrary.org/obo/PCO_0000010 community species richness http://purl.obolibrary.org/obo/PCO_0000004 quality of an ecological community The number of different species represented in an ecological community. http://purl.obolibrary.org/obo/PCO_0000011 population growth http://purl.obolibrary.org/obo/PCO_0000005 population process A process that leads to a change in the number of individuals (positive or negative) in a population. http://purl.obolibrary.org/obo/PCO_0000012 logistic population growth http://purl.obolibrary.org/obo/PCO_0000011 population growth 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. http://purl.obolibrary.org/obo/PCO_0000013 exponential population growth http://purl.obolibrary.org/obo/PCO_0000011 population growth A population growth process that leads to an exponential increase in the number of individuals in a population. http://purl.obolibrary.org/obo/PCO_0000019 community species diversity http://purl.obolibrary.org/obo/PCO_0000004 quality of an ecological community 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. http://purl.obolibrary.org/obo/PCO_0000021 population extinction http://purl.obolibrary.org/obo/PCO_0000005 population process A population process that ultimately leads to the death of all individuals in a population. http://purl.obolibrary.org/obo/PCO_0000022 species extinction http://purl.obolibrary.org/obo/BFO_0000015 process A process that ultimately leads to the death of all individuals in a population. http://purl.obolibrary.org/obo/PCO_0000023 community species evenness http://purl.obolibrary.org/obo/PCO_0000004 quality of an ecological community A quality of an ecological community that reflects how close in abundance all species in a community are. http://purl.obolibrary.org/obo/PCO_0000033 human social gathering activity http://purl.obolibrary.org/obo/GO_0035176 social behavior A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially. http://purl.obolibrary.org/obo/CARO_0001010 organism or virus or viroid http://purl.obolibrary.org/obo/PCO_0000031 organismal entity Material anatomical entity that is a member of an individual species or is a viral or viroid particle. http://purl.obolibrary.org/obo/CARO_0010004 organism http://purl.obolibrary.org/obo/CARO_0001010 organism or virus or viroid An individual member of a clade. http://purl.obolibrary.org/obo/PCO_0000001 population of organisms http://purl.obolibrary.org/obo/PCO_0000018 single-species collection of organisms A collection of organisms, all of the same species, that live in the same place. http://purl.obolibrary.org/obo/PCO_0000017 species as a collection of organisms http://purl.obolibrary.org/obo/PCO_0000059 taxon as collection of organisms A collection of organisms that has as members every organism of given species and no organisms of any other species. http://purl.obolibrary.org/obo/PCO_0000020 family http://purl.obolibrary.org/obo/PCO_0000018 single-species collection of organisms A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption. http://purl.obolibrary.org/obo/PCO_0000024 household http://purl.obolibrary.org/obo/PCO_0000031 organismal entity 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. http://purl.obolibrary.org/obo/PCO_0000029 multi-species collection of organisms http://purl.obolibrary.org/obo/PCO_0000000 collection of organisms A collection of organisms that consists of two or more organisms from at least two species. http://purl.obolibrary.org/obo/PCO_0000030 agricultural household http://purl.obolibrary.org/obo/PCO_0000024 household A household in which the majority of the income of its members is derived from agricultural activities. http://purl.obolibrary.org/obo/PCO_0000031 organismal entity http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity that is one or more organisms, viruses or viroids. http://purl.obolibrary.org/obo/PCO_0001000 pair of interacting organisms http://purl.obolibrary.org/obo/PCO_0000000 collection of organisms A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. http://purl.obolibrary.org/obo/PCO_0001001 pair of interacting organisms of the same species http://purl.obolibrary.org/obo/PCO_0001000 pair of interacting organisms A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. http://purl.obolibrary.org/obo/PCO_0000073 alga excluding Cyanobacteria http://purl.obolibrary.org/obo/CARO_0010004 organism 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. http://purl.obolibrary.org/obo/PCO_0000075 beta diversity http://purl.obolibrary.org/obo/PCO_0000019 community species diversity A community species diversity that is the ratio between regional and local species diversity. http://purl.obolibrary.org/obo/PCO_0000076 gamma diversity http://purl.obolibrary.org/obo/PCO_0000019 community species diversity 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. http://purl.obolibrary.org/obo/PCO_0000078 seedling density http://purl.obolibrary.org/obo/PCO_0000077 plant density The density of seedlings in an ecological community or population, often measured as the number of seedlings per area. http://purl.obolibrary.org/obo/PCO_0000079 plant density of a population http://purl.obolibrary.org/obo/PCO_0000077 plant density The density of plants in a population or organisms (a single species), often measured as the number of plants per area. http://purl.obolibrary.org/obo/PCO_0000080 plant density of an ecological community http://purl.obolibrary.org/obo/PCO_0000077 plant density The density of plants in an ecological community (multiple species), often measured as the number of plants per area. http://purl.obolibrary.org/obo/PCO_0000081 seedling density of a population http://purl.obolibrary.org/obo/PCO_0000078 seedling density The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area. http://purl.obolibrary.org/obo/PCO_0000082 seedling density of an ecological community http://purl.obolibrary.org/obo/PCO_0000078 seedling density The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area. http://purl.obolibrary.org/obo/PCO_0000074 alpha diversity http://purl.obolibrary.org/obo/PCO_0000019 community species diversity A community species diversity that is the mean species diversity at a site or within a specific habitat. http://purl.obolibrary.org/obo/GO_0007610 behavior http://purl.obolibrary.org/obo/GO_0008150 biological_process The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. http://purl.obolibrary.org/obo/GO_0008150 biological_process http://purl.obolibrary.org/obo/BFO_0000015 process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. http://purl.obolibrary.org/obo/GO_0035176 social behavior http://purl.obolibrary.org/obo/GO_0051703 biological process involved in intraspecies interaction between organisms Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. http://purl.obolibrary.org/obo/GO_0051704 multi-organism process http://purl.obolibrary.org/obo/GO_0008150 biological_process A biological process which involves another organism of the same or different species. http://purl.obolibrary.org/obo/GO_0044419 biological process involved in interspecies interaction between organisms http://purl.obolibrary.org/obo/GO_0008150 biological_process Any process evolved to enable an interaction with an organism of a different species. http://purl.obolibrary.org/obo/GO_0051703 biological process involved in intraspecies interaction between organisms http://purl.obolibrary.org/obo/GO_0008150 biological_process Any process in which an organism has an effect on an organism of the same species. http://purl.obolibrary.org/obo/CARO_0000012 multicellular organism http://purl.obolibrary.org/obo/CARO_0010004 organism Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell. http://purl.obolibrary.org/obo/ENVO_01000744 human dwelling http://purl.obolibrary.org/obo/BFO_0000040 material entity A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. http://purl.obolibrary.org/obo/ENVO_01001369 tidal mangrove shrubland http://purl.obolibrary.org/obo/BFO_0000040 material entity A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas. http://purl.obolibrary.org/obo/IAO_8000001 base ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. http://purl.obolibrary.org/obo/IAO_8000003 main release ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. http://purl.obolibrary.org/obo/IAO_8000004 bridge ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. http://purl.obolibrary.org/obo/IAO_8000007 curation subset ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. http://purl.obolibrary.org/obo/IAO_8000008 analysis subset ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module An ontology module that is intended for usage in analysis or discovery applications. http://purl.obolibrary.org/obo/IAO_8000013 reasoned ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. http://purl.obolibrary.org/obo/IAO_8000014 generated ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. http://purl.obolibrary.org/obo/IAO_8000015 template generated ontology module http://purl.obolibrary.org/obo/IAO_8000014 generated ontology module An ontology module that is automatically generated from a template specification and fillers for slots in that template. http://purl.obolibrary.org/obo/IAO_8000018 obo basic subset ontology module http://purl.obolibrary.org/obo/IAO_8000017 ontology module subsetted by expressivity A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports http://purl.obolibrary.org/obo/PCO_1000004 microbial community http://purl.obolibrary.org/obo/PCO_0000051 multi-species collection of microbes 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. http://purl.obolibrary.org/obo/PCO_0000047 tidal mangrove shrubland community http://purl.obolibrary.org/obo/PCO_0000002 ecological community An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. http://purl.obolibrary.org/obo/PCO_0000048 invisible to unaided eye http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. http://purl.obolibrary.org/obo/PCO_0000051 multi-species collection of microbes http://purl.obolibrary.org/obo/PCO_0000029 multi-species collection of organisms A multi-species collection of organisms that consists of two or more microbes from at least two species. http://purl.obolibrary.org/obo/PCO_0000052 single species collection of microbes http://purl.obolibrary.org/obo/PCO_0000050 collection of microbial organisms A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. http://purl.obolibrary.org/obo/PCO_0000053 microbial population http://purl.obolibrary.org/obo/PCO_0000001 population of organisms A population of organisms consisting of only microbes of the same species, that live in the same place. http://purl.obolibrary.org/obo/PCO_0000054 number of generations of multicellular organism http://purl.obolibrary.org/obo/STATO_0000047 count A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism. http://purl.obolibrary.org/obo/PCO_0000057 overcrowded population http://purl.obolibrary.org/obo/PCO_0000003 quality of a population An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels. http://purl.obolibrary.org/obo/PCO_0000058 overcrowded human population http://purl.obolibrary.org/obo/PCO_0000057 overcrowded population A quality of a human population such that the density humans in an area is increased beyond sustainable levels. http://purl.obolibrary.org/obo/PCO_0000059 taxon as collection of organisms http://purl.obolibrary.org/obo/PCO_0000000 collection of organisms 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. http://purl.obolibrary.org/obo/PCO_0000060 microbial parasite http://purl.obolibrary.org/obo/PCO_0000049 microbe An organism or virus or viroid that is a microbe and a parasite. http://purl.obolibrary.org/obo/PCO_0000061 parasite isolate population http://purl.obolibrary.org/obo/PCO_0000053 microbial population 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. http://purl.obolibrary.org/obo/PCO_0000062 Shannon diversity index http://purl.obolibrary.org/obo/PCO_0000019 community species diversity 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). http://purl.obolibrary.org/obo/PCO_0000063 Simpson diversity index http://purl.obolibrary.org/obo/PCO_0000019 community species diversity 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). http://purl.obolibrary.org/obo/PCO_0000064 inverse Simpson diversity index http://purl.obolibrary.org/obo/PCO_0000019 community species diversity 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). http://purl.obolibrary.org/obo/PCO_0000034 human community event http://purl.obolibrary.org/obo/PCO_0000033 human social gathering activity 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. http://purl.obolibrary.org/obo/PCO_0000035 party http://purl.obolibrary.org/obo/PCO_0000033 human social gathering activity 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. http://purl.obolibrary.org/obo/PCO_0000037 potluck http://purl.obolibrary.org/obo/PCO_0000033 human social gathering activity 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. http://purl.obolibrary.org/obo/PCO_0000038 wedding http://purl.obolibrary.org/obo/PCO_0000033 human social gathering activity A human social gathering at which two people are married. May include a legal or social ceremony. http://purl.obolibrary.org/obo/PCO_0000039 baby shower http://purl.obolibrary.org/obo/PCO_0000033 human social gathering activity 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. http://purl.obolibrary.org/obo/IAO_8000000 ontology module http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part ontology file http://purl.obolibrary.org/obo/IAO_8000017 ontology module subsetted by expressivity http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module http://purl.obolibrary.org/obo/PATO_0000068 qualitative http://purl.obolibrary.org/obo/PATO_0000001 quality http://purl.obolibrary.org/obo/PCO_0000077 plant density http://purl.obolibrary.org/obo/PATO_0001019 mass density http://purl.obolibrary.org/obo/PATO_0002062 physical quality of a process http://purl.obolibrary.org/obo/PATO_0001236 process quality http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/GO_0003674 molecular_function http://purl.obolibrary.org/obo/BFO_0000015 process http://purl.obolibrary.org/obo/BFO_0000034 function http://purl.obolibrary.org/obo/BFO_0000016 disposition http://purl.obolibrary.org/obo/BFO_0000016 disposition http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000019 quality http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/IAO_0000030 information content entity http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant http://purl.obolibrary.org/obo/BFO_0000027 object aggregate http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://purl.obolibrary.org/obo/BFO_0000029 site http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://purl.obolibrary.org/obo/NCBITaxon_117571 Euteleostomi http://purl.obolibrary.org/obo/NCBITaxon_117570 Teleostomi http://purl.obolibrary.org/obo/NCBITaxon_8287 Sarcopterygii http://purl.obolibrary.org/obo/NCBITaxon_117571 Euteleostomi http://purl.obolibrary.org/obo/NCBITaxon_3193 Embryophyta http://purl.obolibrary.org/obo/NCBITaxon_131221 Streptophytina http://purl.obolibrary.org/obo/NCBITaxon_2157 Archaea http://purl.obolibrary.org/obo/NCBITaxon_131567 cellular organisms http://purl.obolibrary.org/obo/NCBITaxon_2 Bacteria http://purl.obolibrary.org/obo/NCBITaxon_131567 cellular organisms http://purl.obolibrary.org/obo/NCBITaxon_2759 Eukaryota http://purl.obolibrary.org/obo/NCBITaxon_131567 cellular organisms http://purl.obolibrary.org/obo/NCBITaxon_32523 Tetrapoda http://purl.obolibrary.org/obo/NCBITaxon_1338369 Dipnotetrapodomorpha http://purl.obolibrary.org/obo/NCBITaxon_314146 Euarchontoglires http://purl.obolibrary.org/obo/NCBITaxon_1437010 Boreoeutheria http://purl.obolibrary.org/obo/NCBITaxon_33090 Viridiplantae http://purl.obolibrary.org/obo/NCBITaxon_2759 Eukaryota http://purl.obolibrary.org/obo/NCBITaxon_33154 Opisthokonta http://purl.obolibrary.org/obo/NCBITaxon_2759 Eukaryota http://purl.obolibrary.org/obo/NCBITaxon_9443 Primates http://purl.obolibrary.org/obo/NCBITaxon_314146 Euarchontoglires http://purl.obolibrary.org/obo/NCBITaxon_58023 Tracheophyta http://purl.obolibrary.org/obo/NCBITaxon_3193 Embryophyta http://purl.obolibrary.org/obo/NCBITaxon_32524 Amniota http://purl.obolibrary.org/obo/NCBITaxon_32523 Tetrapoda http://purl.obolibrary.org/obo/NCBITaxon_40674 Mammalia http://purl.obolibrary.org/obo/NCBITaxon_32524 Amniota http://purl.obolibrary.org/obo/NCBITaxon_9347 Eutheria http://purl.obolibrary.org/obo/NCBITaxon_32525 Theria http://purl.obolibrary.org/obo/NCBITaxon_35493 Streptophyta http://purl.obolibrary.org/obo/NCBITaxon_33090 Viridiplantae http://purl.obolibrary.org/obo/NCBITaxon_3041 Chlorophyta http://purl.obolibrary.org/obo/NCBITaxon_33090 Viridiplantae http://purl.obolibrary.org/obo/NCBITaxon_4751 Fungi http://purl.obolibrary.org/obo/NCBITaxon_33154 Opisthokonta http://purl.obolibrary.org/obo/NCBITaxon_33208 Metazoa http://purl.obolibrary.org/obo/NCBITaxon_33154 Opisthokonta http://purl.obolibrary.org/obo/NCBITaxon_6072 Eumetazoa http://purl.obolibrary.org/obo/NCBITaxon_33208 Metazoa http://purl.obolibrary.org/obo/NCBITaxon_33511 Deuterostomia http://purl.obolibrary.org/obo/NCBITaxon_33213 Bilateria http://purl.obolibrary.org/obo/NCBITaxon_7711 Chordata http://purl.obolibrary.org/obo/NCBITaxon_33511 Deuterostomia http://purl.obolibrary.org/obo/NCBITaxon_131221 Streptophytina http://purl.obolibrary.org/obo/NCBITaxon_35493 Streptophyta http://purl.obolibrary.org/obo/NCBITaxon_32525 Theria http://purl.obolibrary.org/obo/NCBITaxon_40674 Mammalia http://purl.obolibrary.org/obo/NCBITaxon_78536 Euphyllophyta http://purl.obolibrary.org/obo/NCBITaxon_58023 Tracheophyta http://purl.obolibrary.org/obo/NCBITaxon_3398 Magnoliopsida http://purl.obolibrary.org/obo/NCBITaxon_58024 Spermatophyta http://purl.obolibrary.org/obo/NCBITaxon_1437180 Acrogymnospermae http://purl.obolibrary.org/obo/NCBITaxon_58024 Spermatophyta http://purl.obolibrary.org/obo/NCBITaxon_33213 Bilateria http://purl.obolibrary.org/obo/NCBITaxon_6072 Eumetazoa http://purl.obolibrary.org/obo/NCBITaxon_89593 Craniata http://purl.obolibrary.org/obo/NCBITaxon_7711 Chordata http://purl.obolibrary.org/obo/NCBITaxon_7776 Gnathostomata http://purl.obolibrary.org/obo/NCBITaxon_7742 Vertebrata http://purl.obolibrary.org/obo/NCBITaxon_117570 Teleostomi http://purl.obolibrary.org/obo/NCBITaxon_7776 Gnathostomata http://purl.obolibrary.org/obo/NCBITaxon_58024 Spermatophyta http://purl.obolibrary.org/obo/NCBITaxon_78536 Euphyllophyta http://purl.obolibrary.org/obo/NCBITaxon_1338369 Dipnotetrapodomorpha http://purl.obolibrary.org/obo/NCBITaxon_8287 Sarcopterygii http://purl.obolibrary.org/obo/NCBITaxon_7742 Vertebrata http://purl.obolibrary.org/obo/NCBITaxon_89593 Craniata http://purl.obolibrary.org/obo/NCBITaxon_1437010 Boreoeutheria http://purl.obolibrary.org/obo/NCBITaxon_9347 Eutheria http://purl.obolibrary.org/obo/PCO_0000049 microbe http://purl.obolibrary.org/obo/CARO_0001010 organism or virus or viroid http://purl.obolibrary.org/obo/GO_0003824 catalytic activity http://purl.obolibrary.org/obo/GO_0003674 molecular_function http://purl.obolibrary.org/obo/GO_0016740 transferase activity http://purl.obolibrary.org/obo/GO_0003824 catalytic activity http://purl.obolibrary.org/obo/GO_0016772 transferase activity, transferring phosphorus-containing groups http://purl.obolibrary.org/obo/GO_0016740 transferase activity http://purl.obolibrary.org/obo/GO_0016301 kinase activity http://purl.obolibrary.org/obo/GO_0016772 transferase activity, transferring phosphorus-containing groups http://purl.obolibrary.org/obo/IAO_8000016 taxonomic bridge ontology module http://purl.obolibrary.org/obo/IAO_8000004 bridge ontology module http://purl.obolibrary.org/obo/IAO_8000019 ontology module subsetted by OWL profile http://purl.obolibrary.org/obo/IAO_8000017 ontology module subsetted by expressivity http://purl.obolibrary.org/obo/IAO_8000020 EL++ ontology module http://purl.obolibrary.org/obo/IAO_8000019 ontology module subsetted by OWL profile http://purl.obolibrary.org/obo/NCBITaxon_9605 Homo http://purl.obolibrary.org/obo/NCBITaxon_207598 Homininae http://purl.obolibrary.org/obo/NCBITaxon_9526 Catarrhini http://purl.obolibrary.org/obo/NCBITaxon_314293 Simiiformes http://purl.obolibrary.org/obo/NCBITaxon_9604 Hominidae http://purl.obolibrary.org/obo/NCBITaxon_314295 Hominoidea http://purl.obolibrary.org/obo/NCBITaxon_314293 Simiiformes http://purl.obolibrary.org/obo/NCBITaxon_376913 Haplorrhini http://purl.obolibrary.org/obo/NCBITaxon_376913 Haplorrhini http://purl.obolibrary.org/obo/NCBITaxon_9443 Primates http://purl.obolibrary.org/obo/NCBITaxon_314295 Hominoidea http://purl.obolibrary.org/obo/NCBITaxon_9526 Catarrhini http://purl.obolibrary.org/obo/NCBITaxon_207598 Homininae http://purl.obolibrary.org/obo/NCBITaxon_9604 Hominidae http://purl.obolibrary.org/obo/NCBITaxon_9606 Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9605 Homo https://purl.obolibrary.org/obo/PCO_0000040 obsolete tidal mangrove shrubland community An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. https://purl.obolibrary.org/obo/PCO_0000041 obsolete invisible to unaided eye A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. https://purl.obolibrary.org/obo/PCO_0000043 obsolete collection of microbial organisms A collection of organisms consisting of two or more microbes. https://purl.obolibrary.org/obo/PCO_0000044 obsolete multi-species collection of microbes A multi-species collection of organisms that consists of two or more microbes from at least two species. https://purl.obolibrary.org/obo/PCO_0000045 obsolete single species collection of microbes A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. https://purl.obolibrary.org/obo/PCO_0000046 obsolete microbial population A population of organisms consisting of only microbes of the same species, that live in the same place. http://purl.obolibrary.org/obo/BFO_0000005 obsolete dependent continuant A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. http://purl.obolibrary.org/obo/PCO_0000009 obsolete carrying capacity The maximum number of individuals that can be supported in a population that is growing according to logistic growth. http://purl.obolibrary.org/obo/pco.owl/PCO_0000030 obsolete organismal entity A material entity that is one or more organisms, viruses or viroids. http://purl.obolibrary.org/obo/PCO_0000028 obsolete community A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. http://purl.obolibrary.org/obo/PCO_0000050 collection of microbial organisms A collection of organisms consisting of two or more microbes. https://purl.obolibrary.org/obo/PCO_0000042 obsolete microbe http://purl.obolibrary.org/obo/NCBITaxon_10239 Viruses http://purl.obolibrary.org/obo/BFO_0000001 entity http://purl.obolibrary.org/obo/NCBITaxon_131567 cellular organisms http://purl.obolibrary.org/obo/PCO_0000014 obsolete predator role http://purl.obolibrary.org/obo/PCO_0000015 obsolete prey role http://purl.obolibrary.org/obo/PCO_0000016 obsolete symbiont role http://purl.obolibrary.org/obo/PCO_0000025 obsolete red population http://purl.obolibrary.org/obo/PCO_0000026 obsolete red organism http://purl.obolibrary.org/obo/RO_0000079 function of http://purl.obolibrary.org/obo/RO_0000052 inheres in is function of a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000080 quality of http://purl.obolibrary.org/obo/RO_0000052 inheres in quality_of a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000085 has function http://purl.obolibrary.org/obo/RO_0000053 bearer of has_function a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000086 has quality http://purl.obolibrary.org/obo/RO_0000053 bearer of has_quality a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0002350 member of http://purl.obolibrary.org/obo/BFO_0000050 part of member part of is member of is a mereological relation between a item and a collection. http://purl.obolibrary.org/obo/RO_0000087 has role http://purl.obolibrary.org/obo/RO_0000053 bearer of has_role a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0002436 molecularly interacts with http://purl.obolibrary.org/obo/RO_0002434 interacts with molecularly binds with An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. http://purl.obolibrary.org/obo/RO_0002449 directly negatively regulates activity of http://purl.obolibrary.org/obo/RO_0002448 directly regulates activity of directly inhibits The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. http://purl.obolibrary.org/obo/BFO_0000062 preceded by http://purl.obolibrary.org/obo/RO_0002086 ends after preceded_by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. http://purl.obolibrary.org/obo/RO_0000081 role of http://purl.obolibrary.org/obo/RO_0000052 inheres in role_of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0002233 has input http://purl.obolibrary.org/obo/RO_0000057 has participant consumes p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. http://purl.obolibrary.org/obo/RO_0002215 capable of http://purl.obolibrary.org/obo/RO_0002216 capable of part of has function realized in A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. http://purl.obolibrary.org/obo/RO_0002331 involved in http://purl.obolibrary.org/obo/RO_0002431 involved in or involved in regulation of enables part of c involved_in p if and only if c enables some process p', and p' is part of p http://purl.obolibrary.org/obo/RO_0002431 involved in or involved in regulation of http://purl.obolibrary.org/obo/RO_0002500 causal agent in process involved in or reguates c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p http://purl.obolibrary.org/obo/RO_0002216 capable of part of http://purl.obolibrary.org/obo/RO_0002500 causal agent in process has function in c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. http://purl.obolibrary.org/obo/RO_0002329 part of structure that is capable of http://purl.obolibrary.org/obo/RO_0002328 functionally related to 0 this relation holds between c and p when c is part of some c', and c' is capable of p. http://purl.obolibrary.org/obo/RO_0002418 causally upstream of or within http://purl.obolibrary.org/obo/RO_0002501 causal relation between processes influences (processual) p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. http://purl.obolibrary.org/obo/RO_0002432 is active in http://purl.obolibrary.org/obo/RO_0002328 functionally related to executes activity in c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. http://purl.obolibrary.org/obo/RO_0002450 directly positively regulates activity of http://purl.obolibrary.org/obo/RO_0002448 directly regulates activity of directly activates The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. http://purl.obolibrary.org/obo/pato#decreased_in_magnitude_relative_to decreased_in_magnitude_relative_to http://purl.obolibrary.org/obo/pato#different_in_magnitude_relative_to different_in_magnitude_relative_to q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. http://purl.obolibrary.org/obo/pato#increased_in_magnitude_relative_to increased_in_magnitude_relative_to http://purl.obolibrary.org/obo/pato#different_in_magnitude_relative_to different_in_magnitude_relative_to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. http://purl.obolibrary.org/obo/BFO_0000063 precedes http://purl.obolibrary.org/obo/RO_0002222 temporally related to x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. http://purl.obolibrary.org/obo/RO_0002351 has member http://purl.obolibrary.org/obo/BFO_0000051 has part has member is a mereological relation between a collection and an item. http://purl.obolibrary.org/obo/RO_0002333 enabled by http://purl.obolibrary.org/obo/RO_0002328 functionally related to inverse of enables http://purl.obolibrary.org/obo/RO_0002404 causally downstream of http://purl.obolibrary.org/obo/RO_0002427 causally downstream of or within inverse of upstream of http://purl.obolibrary.org/obo/RO_0002412 immediately causally upstream of http://purl.obolibrary.org/obo/RO_0002411 causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. http://purl.obolibrary.org/obo/RO_0002448 directly regulates activity of http://purl.obolibrary.org/obo/RO_0011002 regulates activity of The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. http://purl.obolibrary.org/obo/RO_0002566 causally influences http://purl.obolibrary.org/obo/RO_0002506 causal relation between entities The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). http://purl.obolibrary.org/obo/RO_0002263 acts upstream of http://purl.obolibrary.org/obo/RO_0002264 acts upstream of or within c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. http://purl.obolibrary.org/obo/RO_0002131 overlaps http://purl.obolibrary.org/obo/RO_0002323 mereotopologically related to x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/RO_0000091 has disposition http://purl.obolibrary.org/obo/RO_0000053 bearer of a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0011002 regulates activity of http://purl.obolibrary.org/obo/RO_0002566 causally influences The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. http://purl.obolibrary.org/obo/RO_0002411 causally upstream of http://purl.obolibrary.org/obo/RO_0002418 causally upstream of or within p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain http://purl.obolibrary.org/obo/RO_0002211 regulates http://purl.obolibrary.org/obo/RO_0002411 causally upstream of process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. http://purl.obolibrary.org/obo/RO_0002212 negatively regulates http://purl.obolibrary.org/obo/RO_0002211 regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. http://purl.obolibrary.org/obo/RO_0002213 positively regulates http://purl.obolibrary.org/obo/RO_0002211 regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. http://purl.obolibrary.org/obo/RO_0002352 input of http://purl.obolibrary.org/obo/RO_0002328 functionally related to inverse of has input http://purl.obolibrary.org/obo/RO_0002023 directly negatively regulated by http://purl.obolibrary.org/obo/RO_0002022 directly regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. http://purl.obolibrary.org/obo/RO_0002024 directly positively regulated by http://purl.obolibrary.org/obo/RO_0002022 directly regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. http://purl.obolibrary.org/obo/RO_0002264 acts upstream of or within http://purl.obolibrary.org/obo/RO_0002500 causal agent in process c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. http://purl.obolibrary.org/obo/RO_0004031 enables subfunction http://purl.obolibrary.org/obo/RO_0002328 functionally related to Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. http://purl.obolibrary.org/obo/RO_0004034 acts upstream of, positive effect http://purl.obolibrary.org/obo/RO_0004032 acts upstream of or within, positive effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive http://purl.obolibrary.org/obo/RO_0004035 acts upstream of, negative effect http://purl.obolibrary.org/obo/RO_0004033 acts upstream of or within, negative effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative http://purl.obolibrary.org/obo/RO_0002334 regulated by http://purl.obolibrary.org/obo/RO_0002427 causally downstream of or within inverse of regulates http://purl.obolibrary.org/obo/RO_0002335 negatively regulated by http://purl.obolibrary.org/obo/RO_0002334 regulated by inverse of negatively regulates http://purl.obolibrary.org/obo/RO_0002336 positively regulated by http://purl.obolibrary.org/obo/RO_0002334 regulated by inverse of positively regulates http://purl.obolibrary.org/obo/RO_0002427 causally downstream of or within http://purl.obolibrary.org/obo/RO_0002501 causal relation between processes inverse of causally upstream of or within http://purl.obolibrary.org/obo/RO_0002500 causal agent in process http://purl.obolibrary.org/obo/RO_0002595 causal relation between material entity and a process A relationship between a material entity and a process where the material entity has some causal role that influences the process http://purl.obolibrary.org/obo/RO_0002501 causal relation between processes http://purl.obolibrary.org/obo/RO_0002410 causally related to p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. http://purl.obolibrary.org/obo/RO_0002584 has part structure that is capable of http://purl.obolibrary.org/obo/RO_0002595 causal relation between material entity and a process s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p http://purl.obolibrary.org/obo/RO_0002595 causal relation between material entity and a process http://purl.obolibrary.org/obo/RO_0002410 causally related to A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. http://purl.obolibrary.org/obo/RO_0002596 capable of regulating http://purl.obolibrary.org/obo/RO_0002500 causal agent in process Holds between c and p if and only if c is capable of some activity a, and a regulates p. http://purl.obolibrary.org/obo/RO_0002597 capable of negatively regulating http://purl.obolibrary.org/obo/RO_0002596 capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. http://purl.obolibrary.org/obo/RO_0002598 capable of positively regulating http://purl.obolibrary.org/obo/RO_0002596 capable of regulating Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. http://purl.obolibrary.org/obo/RO_0002608 process has causal agent http://purl.obolibrary.org/obo/RO_0002410 causally related to Inverse of 'causal agent in process' http://purl.obolibrary.org/obo/RO_0002428 involved in regulation of http://purl.obolibrary.org/obo/RO_0002431 involved in or involved in regulation of c involved in regulation of p if c is involved in some p' and p' regulates some p http://purl.obolibrary.org/obo/RO_0002429 involved in positive regulation of http://purl.obolibrary.org/obo/RO_0002428 involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p http://purl.obolibrary.org/obo/RO_0002430 involved in negative regulation of http://purl.obolibrary.org/obo/RO_0002428 involved in regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p http://purl.obolibrary.org/obo/RO_0002578 directly regulates http://purl.obolibrary.org/obo/RO_0002211 regulates Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. http://purl.obolibrary.org/obo/RO_0002629 directly positively regulates http://purl.obolibrary.org/obo/RO_0002578 directly regulates Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. http://purl.obolibrary.org/obo/RO_0002630 directly negatively regulates http://purl.obolibrary.org/obo/RO_0002578 directly regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. http://purl.obolibrary.org/obo/RO_0002087 immediately preceded by http://purl.obolibrary.org/obo/BFO_0000062 preceded by starts_at_end_of http://purl.obolibrary.org/obo/RO_0002090 immediately precedes http://purl.obolibrary.org/obo/BFO_0000063 precedes meets http://purl.obolibrary.org/obo/RO_0002327 enables http://purl.obolibrary.org/obo/RO_0002215 capable of is executing http://purl.obolibrary.org/obo/RO_0002447 phosphorylates http://purl.obolibrary.org/obo/RO_0002436 molecularly interacts with An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. http://purl.obolibrary.org/obo/RO_0000092 disposition of http://purl.obolibrary.org/obo/RO_0000052 inheres in http://purl.obolibrary.org/obo/RO_0002405 immediately causally downstream of http://purl.obolibrary.org/obo/RO_0002404 causally downstream of http://purl.obolibrary.org/obo/RO_0002559 causally influenced by http://purl.obolibrary.org/obo/RO_0002506 causal relation between entities http://purl.obolibrary.org/obo/RO_0002563 interaction relation helper property http://purl.obolibrary.org/obo/RO_0002464 helper property (not for use in curation) http://purl.obolibrary.org/obo/RO_0002564 molecular interaction relation helper property http://purl.obolibrary.org/obo/RO_0002563 interaction relation helper property http://purl.obolibrary.org/obo/RO_0002481 is kinase activity http://purl.obolibrary.org/obo/RO_0002564 molecular interaction relation helper property http://purl.obolibrary.org/obo/RO_0002086 ends after http://purl.obolibrary.org/obo/RO_0002222 temporally related to http://purl.obolibrary.org/obo/RO_0002304 causally upstream of, positive effect http://purl.obolibrary.org/obo/RO_0004047 causally upstream of or within, positive effect http://purl.obolibrary.org/obo/RO_0002305 causally upstream of, negative effect http://purl.obolibrary.org/obo/RO_0004046 causally upstream of or within, negative effect http://purl.obolibrary.org/obo/RO_0004033 acts upstream of or within, negative effect http://purl.obolibrary.org/obo/RO_0002264 acts upstream of or within http://purl.obolibrary.org/obo/RO_0004032 acts upstream of or within, positive effect http://purl.obolibrary.org/obo/RO_0002264 acts upstream of or within http://purl.obolibrary.org/obo/RO_0002022 directly regulated by http://purl.obolibrary.org/obo/RO_0002334 regulated by http://purl.obolibrary.org/obo/RO_0002506 causal relation between entities http://purl.obolibrary.org/obo/RO_0002410 causally related to http://purl.obolibrary.org/obo/RO_0004046 causally upstream of or within, negative effect http://purl.obolibrary.org/obo/RO_0002418 causally upstream of or within http://purl.obolibrary.org/obo/RO_0004047 causally upstream of or within, positive effect http://purl.obolibrary.org/obo/RO_0002418 causally upstream of or within http://purl.obolibrary.org/obo/RO_0000052 inheres in inheres_in a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000053 bearer of is bearer of a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000056 participates in participates_in a relation between a continuant and a process, in which the continuant is somehow involved in the process http://purl.obolibrary.org/obo/RO_0000057 has participant has_participant a relation between a process and a continuant, in which the continuant is somehow involved in the process http://purl.obolibrary.org/obo/RO_0001000 derives from derives_from a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity http://purl.obolibrary.org/obo/RO_0001001 derives into derives_into a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity http://purl.obolibrary.org/obo/RO_0001015 location of location_of a relation between two independent continuants, the location and the target, in which the target is entirely within the location http://purl.obolibrary.org/obo/RO_0002000 2D boundary of is boundary of a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity http://purl.obolibrary.org/obo/RO_0002002 has 2D boundary has_2D_boundary a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity http://purl.obolibrary.org/obo/RO_0001025 located in located_in a relation between two independent continuants, the target and the location, in which the target is entirely within the location http://purl.obolibrary.org/obo/BFO_0000051 has part has_part a core relation that holds between a whole and its part http://purl.obolibrary.org/obo/BFO_0000050 part of part_of a core relation that holds between a part and its whole http://purl.obolibrary.org/obo/BFO_0000066 occurs in unfolds_in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t http://purl.obolibrary.org/obo/pato#different_in_magnitude_relative_to different_in_magnitude_relative_to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. http://purl.obolibrary.org/obo/pato#reciprocal_of reciprocal_of q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. http://purl.obolibrary.org/obo/BFO_0000067 contains process [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t http://purl.obolibrary.org/obo/IAO_0000136 is about A (currently) primitive relation that relates an information artifact to an entity. http://purl.obolibrary.org/obo/RO_0000058 is concretized as A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. http://purl.obolibrary.org/obo/RO_0000059 concretizes A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. http://purl.obolibrary.org/obo/RO_0002434 interacts with A relationship that holds between two entities in which the processes executed by the two entities are causally connected. http://purl.obolibrary.org/obo/RO_0002323 mereotopologically related to A mereological relationship or a topological relationship http://purl.obolibrary.org/obo/RO_0002328 functionally related to A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. http://purl.obolibrary.org/obo/RO_0002321 ecologically related to A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) http://purl.obolibrary.org/obo/RO_0002410 causally related to This relation groups causal relations between material entities and causal relations between processes http://purl.obolibrary.org/obo/RO_0002479 has part that occurs in p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. http://purl.obolibrary.org/obo/BFO_0000054 realized in realized_in http://purl.obolibrary.org/obo/BFO_0000055 realizes http://purl.obolibrary.org/obo/RO_0002464 helper property (not for use in curation) http://purl.obolibrary.org/obo/RO_0002222 temporally related to http://purl.obolibrary.org/obo/PCO_0000055 obsolete has member of