Ramona Walls 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. http://creativecommons.org/publicdomain/zero/1.0/ editor preferred term example of usage has curation status definition definition editor note term editor alternative term definition source curator note imported from expand expression to expand assertion to first order logic expression OBO foundry unique label temporal interpretation https://code.google.com/p/obo-relations/wiki/ROAndTime never in taxon x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. ?X DisjointWith RO_0002162 some ?Y tooth SubClassOf 'never in taxon' value 'Aves' Chris Mungall PMID:17921072 PMID:20973947 shorthand part of Intended meaning: Ambiguous between continuant-parthood and occurrent-parthood. domain: continuant range: continuant time: at some time domain: occurrent range: occurrent time: atemporal Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell. http://www.obofoundry.org/ro/#OBO_REL:part_of part of part_of has part Intended meaning: Ambiguous between continuant-parthood and occurrent-parthood. domain: continuant range: continuant time: at some time domain: occurrent range: occurrent time: atemporal has part has_part realized in Intended meaning: domain: realizable entity range: processual entity time: atemporal is realized by realized in realized_in realizes Intended meaning: domain: processual entity range: realizable entity time: atemporal realizes preceded by An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. Intended meaning: domain: occurrent range: occurrent time: atemporal http://www.obofoundry.org/ro/#OBO_REL:preceded_by is preceded by preceded by preceded_by precedes Intended meaning: domain: occurrent range: occurrent time: atemporal precedes occurs in Intended meaning: domain: occurrent range: independent continuant time: atemporal occurs in occurs_in unfolds in unfolds_in contains process site of inheres in Intended meaning: domain: specifically dependent continuant range: independent continuant time: at all times A specifically dependent continuant A inheres in its independent continuant B at all times during which A exists. inheres in inheres_in bearer of Intended meaning: domain: independent continuant range: specifically dependent continuant time: at some time bearer of bearer_of is bearer of participates in Intended meaning: domain: continuant and (not spatial region) range: processual entity time: at some time participates in participates_in has participant has participant has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. Intended meaning: domain: processual entity range: continuant and (not spatial region) time: at some time derives from See also BFO_0001009 derives into location of location of location_of contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained in contained_in contains Intended meaning: domain: spatial region or site (immaterial continuant) range: material entity contains located in Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus http://www.obofoundry.org/ro/#OBO_REL:located_in located in located_in before_or_simultaneous_with <= Primitive instance level timing relation between events simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) before t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) during_which_ends Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. encompasses di Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. ends_after X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) starts_at_end_of during_which_starts Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. starts_before immediately_precedes meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) ends_at_start_of starts_during X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) io happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) during d ends_during X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). overlaps o overlaps 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/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) connected to David Osumi-Sutherland X connected_to Y if and only if X and Y share a fiat boundary. Consider relabeling this to "continuous with" (FMA:85972). The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) proper overlaps (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x))))) partially overlaps spatially disjoint from A is spatially_disjoint_from B if and only if they have no parts in common BFO_0000051 exactly 0 (BFO_0000050 some ?Y) Chris Mungall There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. has component For use in recording has_part with a cardinality constraint. actively participates in x actively participates in y if and only if x participates in y and x realizes some active role agent in has active participant x has participant y if and only if x realizes some active role that inheres in y has agent surrounded by x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y adjacent to x adjacent to y if and only if x and y share a boundary TODO: replaced by BFO_0001008 belongs in BFO? surrounds temporally related to https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 Allen A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. starts Allen Chris Mungall inverse of starts with starts with Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(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. started by ends inverse of ends with ends with finished by x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(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. has input has output inheres in part of mereotopologically related to Chris Mungall A mereological relationship or a topological relationship member of is member of member part of SIO An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. has member SIO has member is a mereological relation between a collection and an item. input of output of formed as result of organism or virus or viroid 9/18/11 Material anatomical entity that is a member of an individual species or is a viral or viroid particle. Melissa Haendel organism or virus organism 7.16.2011 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. An individual member of a clade. mah organism collection of organisms A material entity that consists of two or more organisms, viruses, or viroids. Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. May be of the same or different species. group of organism organism collection population A collection of organisms, all of the same species, that live in the same place. ISBN:0878932739 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. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across ontologies and only one term used. Still uncertain if this should include every organism of a species living in an area or any subset of them. For now make this a general term (unspecified) and then subclasses can be more specific. ecological community A collection of organisms of at least two different species, living in a particular area. Ecological community is defined broadly here. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The work community, as it often used to describe a group of humans living together, is a type of population (PCO_0000001). ISBN:0865423504 multispecies community population quality A quality that inheres in a biological population. 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. 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. community quality A quality that inheres in a community. 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. These may not belong under BFO:quality. population 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. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. population birth rate population death rate population growth rate Is a rate a quality? Population growth rate may be better classified as a process profile. carrying capacity The maximum number of individuals that can be supported in a population that is growing according to logistic growth. ISBN:0878932739 Might be better to add this as a data property. community species richness This term is specific to an ecological community (PCO_0000002). Species richness can also be measured for a geographical area or region. If your metric includes the abundances of species as well as the number, you should use community species diversity (PCO_0000019). adapted from http://en.wikipedia.org/wiki/Species_richness The number of different species represented in an ecological community. population growth A process that leads to a change in the number of individuals (positive or negative) in a population. logistic 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. exponential population growth A population growth process that leads to an exponential increase in the number of individuals in a population. predator role prey role symbiont role species as a collection of organisms. A collection of organisms that has as parts every organism of given species and no organisms of any other species. 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. collection of organisms of the same species need equivalentTo axiom 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. community species diversity This term is specific to an ecological community (PCO_0000002). Species diversity can also be measured for a geographical area or region. If your metric does not include the abundances of different species, you should use community species richness (PCO_0000010). The number of equally-abundant species needed to obtain the same mean proportional species abundance as that observed in a population (where all species may not be equally abundant). Species diversity consists of two components, species richness and species evenness. add another definition source adapted from http://en.wikipedia.org/wiki/Species_diversity family A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption. Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 population extinction A population process that ultimately leads to the death of all individuals in a population. species extinction A process that ultimately leads to the death of all individuals in a population. community species evenness http://en.wikipedia.org/wiki/Species_evenness How close in numbers each species in a community are. axiom holds for all times ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation relation has no temporal argument ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y) term replaced by curation status specification pending final vetting requires discussion obsolescence reason specification