Human ancestry ontology for the NHGRI GWAS Catalog Human Ancestry Ontology 2024-02-07 editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition term editor alternative_term definition_source has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. Nicolas Matentzoglu has ontology root term term replaced by If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive database_cross_reference has_exact_synonym is defined by is defined by This is an experimental annotation label is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of https://wiki.geneontology.org/Part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part has_part 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. 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. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes 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. precedes hasEthnicPopulation true hasAncestryStatus hasCountryOfOrigin hasDemonym isDemonymOf inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of has characteristic participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process 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. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ location_of location of location_of located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location 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 Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in located_in https://wiki.geneontology.org/Located_in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. 2017-05-24T09:49:21Z has component process 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) 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. directly regulated by Process(P2) is directly regulated by process(P1) 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. 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. 2017-09-17T13:52:38Z directly negatively 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. 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. 2017-09-17T13:52:47Z directly positively 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. A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes 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) overlaps true w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. negatively regulates (process to process) negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. positively regulates (process to process) positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' 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. has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". capable of 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. has function in capable of part of true Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to 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. consumes has input https://wiki.geneontology.org/Has_input A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. 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. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. 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. affects acts upstream of or within https://wiki.geneontology.org/Acts_upstream_of_or_within p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. causally upstream of, negative effect q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of inheres in part of characteristic of part of true A mereological relationship or a topological relationship Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables https://wiki.geneontology.org/Enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. false part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p actively involved in enables part of involved in https://wiki.geneontology.org/Involved_in inverse of enables enabled by https://wiki.geneontology.org/Enabled_by inverse of regulates regulated by (processual) regulated by inverse of negatively regulates negatively regulated by inverse of positively regulates positively regulated by inverse of has input input of A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with inverse of upstream of causally downstream of immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. indirectly activates indirectly positively regulates https://wiki.geneontology.org/Indirectly_positively_regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly inhibits indirectly negatively regulates https://wiki.geneontology.org/Indirectly_negatively_regulates relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. https://en.wikipedia.org/wiki/Causality p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. causally upstream of p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. immediately causally upstream of p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 influences (processual) affects causally upstream of or within inverse of causally upstream of or within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p involved in negative regulation of 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 OWL does not allow defining object properties via a Union involved in or reguates involved in or involved in regulation of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Considering relabeling as 'pairwise interacts with' Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 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. binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates 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. molecularly controls directly regulates activity of 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. directly inhibits molecularly decreases activity of directly negatively regulates activity of 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. directly activates molecularly increases activity of directly positively regulates activity of This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) is kinase activity A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process 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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities causally influenced by (entity-centric) causally influenced by interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ molecular interaction relation helper property 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). causally influences (entity-centric) causally influences p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' 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 has part structure that is capable of 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. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) directly positively regulates https://wiki.geneontology.org/Directly_positively_regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) directly negatively regulates https://wiki.geneontology.org/Directly_negatively_regulates Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. 2018-01-25T23:20:13Z enables subfunction 2018-01-26T23:49:30Z acts upstream of or within, positive effect https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect 2018-01-26T23:49:51Z acts upstream of or within, negative effect https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_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 2018-01-26T23:53:14Z acts upstream of, positive effect https://wiki.geneontology.org/Acts_upstream_of,_positive_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 2018-01-26T23:53:22Z acts upstream of, negative effect https://wiki.geneontology.org/Acts_upstream_of,_negative_effect 2018-03-13T23:55:05Z causally upstream of or within, negative effect https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect 2018-03-13T23:55:19Z causally upstream of or within, positive effect 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. regulates activity of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. 2022-09-26T06:07:17Z indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. 2022-09-26T06:08:01Z indirectly regulates A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. negatively regulates characteristic GAZ:00006882 Afghanistan GAZ:00000457 Africa GAZ:00002953 Albania GAZ:00000563 Algeria GAZ:00003957 American Samoa GAZ:00002948 Andorra GAZ:00001095 Angola GAZ:00009159 Anguilla GAZ:00006883 Antigua and Barbuda GAZ:00002928 Argentina GAZ:00004094 Armenia GAZ:00004025 Aruba GAZ:00000465 Asia GAZ:00000463 Australia GAZ:00002942 Austria GAZ:00004941 Azerbaijan GAZ:00005281 Bahrain GAZ:00003750 Bangladesh GAZ:00001251 Barbados GAZ:00006886 Belarus GAZ:00002938 Belgium GAZ:00002934 Belize GAZ:00000904 Benin GAZ:00001264 Bermuda GAZ:00003920 Bhutan GAZ:00002511 Bolivia GAZ:00006887 Bosnia and Herzegovina GAZ:00001097 Botswana GAZ:00002828 Brazil GAZ:00003961 British Virgin Islands GAZ:00003901 Brunei Darussalam Brunei GAZ:00002950 Bulgaria GAZ:00000905 Burkina Faso GAZ:00001090 Burundi GAZ:00006888 Cambodia GAZ:00001093 Cameroon GAZ:00002560 Canada GAZ:00001227 Cape Verde Caribbean GAZ:00003986 Cayman Islands Middle Africa GAZ:00000588 Central Africa GAZ:00001089 Central African Republic GAZ:00002891 Central America GAZ:00000586 Chad GAZ:00001539 Channel Islands GAZ:00002825 Chile GAZ:00002845 China GAZ:00005915 Christmas Island GAZ:00002929 Colombia GAZ:00005820 Comoros GAZ:00053798 Cook Islands GAZ:00002901 Costa Rica GAZ:00002719 Croatia GAZ:00003762 Cuba GAZ:00012582 Curacao GAZ:00453362 Cyprus GAZ:00002954 Czech Republic GAZ:00001086 Democratic Republic of the Congo GAZ:00002635 Denmark GAZ:00000582 Djibouti GAZ:00006890 Dominica GAZ:00003952 Dominican Republic GAZ:00006913 Timor-Leste East Timor GAZ:00000556 Eastern Africa GAZ:00002471 Eastern Asia Eastern Europe GAZ:00002912 Ecuador GAZ:00003934 Egypt GAZ:00002935 El Salvador GAZ:00001091 Equatorial Guinea GAZ:00000581 Eritrea GAZ:00002959 Estonia GAZ:00001099 Eswatini GAZ:00000567 Ethiopia GAZ:00000464 Europe Faroe Islands GAZ:00059206 Faeroe Islands GAZ:00001412 Falkland Islands (Malvinas) Falkland Islands GAZ:00006897 Micronesia (Federated States of) GAZ:00006891 Fiji GAZ:00002937 Finland GAZ:00002940 France GAZ:00002516 French Guiana GAZ:00002918 French Polynesia GAZ:00001092 Gabon GAZ:00002646 Germany GAZ:00000908 Ghana GAZ:00003987 Gibraltar GAZ:00002945 Greece GAZ:00001507 Greenland GAZ:02000573 Grenada GAZ:00067135 Guadeloupe GAZ:00006933 Guam GAZ:00002936 Guatemala GAZ:00000909 Guinea GAZ:00000910 Guinea-Bissau GAZ:00002522 Guyana GAZ:00003953 Haiti GAZ:00003103 Holy See GAZ:00002894 Honduras GAZ:00003203 China, Hong Kong SAR Hong Kong GAZ:00002952 Hungary GAZ:00000843 Iceland GAZ:00002839 India GAZ:00003727 Indonesia GAZ:00004474 Iran (Islamic Republic of) Iran GAZ:00004483 Iraq GAZ:00052477 Isle of Man GAZ:00002476 Israel GAZ:00002650 Italy GAZ:00000906 Ivory Coast Côte d'Ivoire GAZ:00003781 Jamaica GAZ:00002747 Japan GAZ:00002473 Jordan GAZ:00004999 Kazakhstan GAZ:00001101 Kenya GAZ:00006894 Kiribati GAZ:00011337 Kosovo GAZ:00005285 Kuwait GAZ:00006893 Kyrgyzstan GAZ:00006889 Lao People's Democratic Republic Laos GAZ:00000459 Latin America and the Caribbean GAZ:00002958 Latvia GAZ:00002478 Lebanon GAZ:00001098 Lesotho GAZ:00000911 Liberia GAZ:00000566 Libyan Arab Jamahiriya Libya GAZ:00003858 Liechtenstein GAZ:00002960 Lithuania GAZ:00002947 Luxembourg GAZ:00003202 China, Macao SAR Macau GAZ:00001108 Madagascar GAZ:00001105 Malawi GAZ:00003902 Malaysia GAZ:00006896 Maldives GAZ:00000584 Mali GAZ:00004017 Malta GAZ:00007161 Marshall Islands GAZ:00003947 Martinique GAZ:00000583 Mauretania Mauritania GAZ:00003745 Mauritius GAZ:00003943 Mayotte GAZ:00005860 Melanesia GAZ:00002852 Mexico GAZ:00005862 Micronesia http://dbpedia.org/resource/Central_Africa true GAZ:00003897 Republic of Moldova Moldova GAZ:00003857 Monaco GAZ:00008744 Mongolia GAZ:00006898 Montenegro GAZ:00003988 Montserrat GAZ:00000565 Morocco GAZ:00001100 Mozambique GAZ:00006899 Burma Myanmar GAZ:00001096 Namibia GAZ:00006900 Nauru GAZ:00004399 Nepal GAZ:00001549 Netherlands GAZ:00004019 Netherlands Antilles GAZ:00005206 New Caledonia GAZ:00000469 New Zealand GAZ:00002978 Nicaragua GAZ:00000585 Niger GAZ:00000912 Nigeria Niue Fekai GAZ:00006902 Niue GAZ:00005913 Norfolk Island GAZ:00002801 Democratic People's Republic of Korea North Korea GAZ:00000555 Northern Africa GAZ:00000458 Northern America Northern Europe GAZ:00003958 Northern Mariana Islands Kingdom of Norway GAZ:00002699 Norway GAZ:00000468 Oceania GAZ:00005283 Oman GAZ:00005246 Pakistan GAZ:00006905 Palau GAZ:00002475 Occupied Palestinian Territory Palestinian Territories GAZ:00002892 Panama GAZ:00003922 Papua New Guinea GAZ:00002933 Paraguay GAZ:00002932 Peru The Philippines GAZ:00004525 Philippines Pitcairn GAZ:00005867 Pitcairn, Henderson, Ducie and Oeno Islands Pitcairn Islands GAZ:00002939 Poland GAZ:00005861 Polynesia Portugese Republic GAZ:00002944 Portugal Commonwealth of Puerto Rico GAZ:00006935 Puerto Rico GAZ:00005286 Qatar GAZ:00002943 Ireland Republic of Ireland GAZ:00006895 The former Yugoslav Republic of Macedonia Republic of Macedonia GAZ:00001088 Congo Republic of the Congo GAZ:00002951 Romania GAZ:00002721 Russian Federation Russia GAZ:00001087 Rwanda GAZ:00053746 Réunion GAZ:00000849 St. Helena Saint Helena GAZ:00006906 Saint Kitts and Nevis GAZ:00006909 Saint Lucia GAZ:00005841 Saint Martin GAZ:00003942 Saint-Pierre-et-Miquelon Saint Pierre and Miquelon GAZ:02000565 Saint Vincent and the Grenadines GAZ:00006910 Samoa GAZ:00003102 San Marino GAZ:00005279 Saudi Arabia Scandinavia GAZ:00002639 Scotland GAZ:00000913 Senegal GAZ:00002957 Serbia GAZ:00005821 Seychelles GAZ:00000914 Sierra Leone GAZ:00003923 Singapore GAZ:00012579 Sint Maarten GAZ:00002956 Slovakia GAZ:00002955 Slovenia GAZ:00005275 Solomon Islands GAZ:00001104 Somalia GAZ:00000559 South-Eastern Asia South-Central Asia GAZ:00000459 South America GAZ:00000553 South Africa GAZ:00002472 South Asia GAZ:00002802 Republic of Korea South Korea GAZ:00233439 South Sudan GAZ:00000553 Southern Africa Southern Europe GAZ:00000591 Spain GAZ:00003924 Sri Lanka GAZ:00000560 Sudan GAZ:00002525 Suriname http://dbpedia.org/resource/Eswatini obsolete Swaziland true GAZ:00002729 Sweden GAZ:00002941 Switzerland GAZ:00002474 Syria GAZ:00006927 São Tomé and Príncipe GAZ:00005341 Taiwan GAZ:00006912 Tajikistan GAZ:00001103 United Republic of Tanzania Tanzania GAZ:00003744 Thailand GAZ:00002733 Bahamas The Bahamas GAZ:00000907 Gambia The Gambia GAZ:00000915 Togo GAZ:00006914 Tokelau GAZ:00006916 Tonga GAZ:00003767 Trinidad and Tobago GAZ:00000562 Tunisia GAZ:00000558 Turkey GAZ:00005018 Turkmenistan GAZ:00003955 Turks and Caicos Islands GAZ:00009715 Tuvalu GAZ:00001102 Uganda GAZ:00002724 Ukraine GAZ:00005282 United Arab Emirates GAZ:00002637 U.K. United Kingdom U.S. GAZ:00002459 United States of America United States GAZ:00003959 U.S. Virgin Islands United States Virgin Islands GAZ:00002930 Uruguay GAZ:00004979 Uzbekistan GAZ:00006918 Vanuatu GAZ:00002931 Venezuela GAZ:00003756 Vietnam GAZ:00007191 Wallis and Futuna Islands Wallis and Futuna GAZ:00000554 Western Africa Western Asia Western Europe GAZ:00000564 Western Sahara GAZ:00005284 Yemen GAZ:00001107 Zambia GAZ:00001106 Zimbabwe GAZ:00009721 Cocos (Keeling) Islands GAZ:00004942 Georgia entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant 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. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] An entity that has temporal parts and that happens, unfolds or develops through time. occurrent ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] spatial region p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process disposition 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. realizable entity quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] 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. specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] 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. role function material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] immaterial entity geographical location One of the large, unbroken masses of land into which the Earth's surface is divided. major area continent true Any geographic area greater than an individual country but smaller than a continent, used as a convenience reference. Please note that most geographic areas may not be formally defined and exact boundaries can be debatable. geographical area region A collective generic term that refers here to a wide variety of dependencies, areas of special sovereignty, uninhabited islands, and other entities in addition to the traditional countries or independent states. NCIT:C25464 http://purl.obolibrary.org/obo/NCIT_C25464 obsolete country true Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data ancestral group ancestry category Includes individuals who either self-report or have been described by authors as European, Caucasian, White or one of the sub-populations from this region (e.g Dutch). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CEU, FIN, GBR, IBS and TSI populations. Caucasian white European Includes individuals who either self-report or have been described by authors as South Asian or one of the sub-populations from this region (e.g Asian Indian). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap BEB, GIH, ITU, PJL and STU populations. South Asian Includes individuals who either self-report or have been described by authors as South East Asian or one of the sub-populations from this region (e.g Vietnamese). This category also includes includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes KHV population. We note that East Asian and South East Asian populations are often conflated. However, recent studies indicate a unique genetic background for South East Asian populations. South East Asian Includes individuals that either self-report or have been described as Asian but there was not sufficient information to allow classification as East Asian, Central Asian, South Asian or South-East Asian. Asian unspecified Asian Includes individuals who either self-report or have been described by authors as East Asian or one of the sub-populations from this region (e.g Chinese). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CDX, CHB, CHS and JPT populations. East Asian Includes individuals that either self-report or have been described as African, but there was not sufficient information to allow classification as African American, AfroCaribbean or Sub-Saharan African. African unspecified African Includes individuals who either self-report or have been described by authors as SubSaharan African or one of the subpopulations from this region (e.g. Yoruban). This category also includes individuals who genetically cluster with reference populations from this region for example 1000 Genomes and/or HapMap ESN, LWK, GWD, MSL, MKK and YRI populations. Sub-Saharan African Includes indigenous individuals of North, Central and South America, descended from the original human migration into the Americas from Siberia. We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap. American Indian Native American Includes individuals who either self-report or are described by authors as Hispanic, Latino, Latin American or one of the sub-populations from this region. This category includes individuals with known admixture of primarily European, African and Native American ancestries, though some may have also a degree of Asian (e.g. Peru). We also note that the levels of admixture vary depending on the country, with Caribbean countries carrying higher levels of African admixture when compared to South American countries, for example. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CLM, MXL, PEL and PUR populations Jackie MacArthur Joannella Morales Hispanic or Latin American Includes individuals who self-report or were described by authors as Middle Eastern, North African, Persian or one of the subpopulations from this region (e.g. Saudi Arabian). We note there is heterogeneity in this category with different degrees of admixture as well as levels of genetic isolation. We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap. Middle Eastern/North African Greater Middle Eastern (Middle Eastern or North African or Persian) Includes individuals who either self-report or have been described by authors as African American or Afro-Caribbean. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap ACB or ASW populations. We note that there is likely to be significant admixture with European ancestry populations. African American or Afro-Caribbean Includes individuals that either self-report or have been described by authors as Oceanian or one of the sub-populations from this region (e.g. Native Hawaiian). We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap. Oceanian A population for which specific ancestry information is known but that does not fall into any of the defined ancestry categories uncategorised population Japanese non-aboriginal Taiwanese Taiwanese Chinese Korean Mongolian Macanese Singaporean Chinese Hong Kong Chinese Han Chinese obsolete Africa true obsolete Asia true obsolete Europe true obsolete Oceania true obsolete Latin America and the Caribbean true obsolete Northern America true obsolete Eastern Africa true obsolete Middle Africa true obsolete Northern Africa true obsolete Southern Africa true obsolete Western Africa true obsolete South Central Asia true obsolete South-Eastern Asia true obsolete Western Asia true obsolete Eastern Europe true obsolete Northern Europe true obsolete Southern Europe true obsolete Western Europe true obsolete Caribbean true obsolete South America true obsolete Central America true Australia/New Zealand obsolete Melanesia true obsolete Micronesia true obsolete Polynesia true obsolete Eastern Asia true Includes individuals who either self-report or have been described by authors as Central Asian. We note that there does not appear to be a suitable reference population for this population and efforts are required to fill this gap. Central Asian obsolete Scandinavia true obsolete South Asia true A population with increased genetic homogeneity and reduced genetic variation due to cultural or geographic isolation founder population population isolate genetically isolated population General characterisation of the ancestry of a population or individual ancestry status ancestry status Ancestry that is the result of cultural or geographic isolation. Generally characterised by increased genetic homogeneity and reduced genetic variation genetically isolated ancestry Ancestry which is an admixture of more than one defined ancestral population. The degree and type of admixture may vary within a population and the accuracy of classification requires well-defined reference samples admixed ancestry Italian Sardinian Val Borbera Friuli Venezia Giulia Carlantino Old Order Amish Sorbian Hutterite Amish Erasmus Rucphen Orcadian Korculan Dutch Finnish Finnish founder Dutch founder Ashkenazi Jew obsolete_Caribbean true Sudanese Sahrawi Anguillan Antiguan or Barbudan Barbadian Haitian Jamaican Tajikistani Turkmen Uzbekistani Afghan Kazakhstani Kyrgyzstani Albanian Andorran Australian Austrian Belarusian Belgian Bermudian Bosnian or Herzegovinian Brazilian Bulgarian Canadian Channel Islander Chilean Croatian Czech Danish Estonian Faroese Falkland Islander French German Gibraltarian Greek Greenlander Hungarian Icelandic Manx Latvian Liechtensteiner Lithuanian Luxembourgish Maltese Monegasque Montenegrin New Zealandish Norfolk Islander Norwegian Polish Portugese Irish Moldovan Romanian Russian Saint-Pierrais or Miquelonnais Sammarinese Serb Slovak Slovene Spanish Swedish Swiss Macedonian Ukrainian Argentine Bahamian Belizean Bolivian British Virgin Islander Caymanian Colombian Costa Rican Cuban Dominican Ecuadorian Salvadoran French Guianese Grenadian Guatemalan Guyanese Honduran Martinican Mexican Montserratian Nicaraguan Panamanian Paraguayan Peruvian Puerto Rican Kittitian or Nevisian Saint Lucian Saint Vincentian Surinamer Surinamese Trinidadian or Tobagonian Turks and Caicos Islander Virgin Islander Uruguayan Venezuelan Algerian Armenian Azerbaijani Bahraini Cypriote Egyptian Georgian Iranian Iraqi Israeli Jordanian Kuwaiti Lebanese Libyan Moroccan Palestinian Omani Qatari Saudi Arab Saudi Tunisian Turkish Emirati Yemeni Aruban Christmas Islander Cocos Islander Curacaoan Kosovar Northern Mariana Islander South Sudanese Syrian British American American Samoan Cook Islander Fijian French Polynesian Guamanian I-Kiribati Marshallese Micronesian Nauruan New Caledonian Niuean Palauan Papua New Guinean Pitcairn Islander Samoan Solomon Islander Tokelauan Tongan Tuvaluan Ni-Vanuato Wallis and Futuna Islander Bangladeshi Bhutanese Asian Indian Indian Asian Indian Maldivian Nepalese Pakistani Sri Lankan Bruneian Cambodian Indonesian Lao Malaysian Burmese Filipino Thai Timorese Vietnamese Cameroonian Cape Verdean Chadian Ethiopian Kenyan Liberian Malagasy Mauritanian Mauritian Mahoran Namibian Sao Tomean Senegalese Seychellois Sierra Leonean Somali South African St. Helenian Ugandan Angolan Beninese Motswana Burkinabe Burundian Central African Comoran Congolese Ivoirian Djiboutian Equatorial Guinean Eritrean Gabonese Gambian Ghanaian Guinean Bissau-Guinean Mosotho Malawian Malian Mozambican Nigerien Nigerian Rwandan Swazi Togolese Tanzanian Zambian Zimbabweian Irish founder genetically homogenous Irish Includes individuals who either self-report or have been described by authors as Australian Aboriginal. These are expected to be descendents of early human migration into Australia from Eastern Asia and can be distinguished from other Asian populations by mtDNA and Y chromosome variation. Aboriginal Australian Includes native populations of Alaska, Siberia, and the Aleutian Archipelago. This category does not include all native populations within the Arctic circle for example the Finnish Saami who are descended from Europeans and are therefore included within the European ancestry category. obsolete_Circumpolar people true Silk Road founder Israeli Arab Arab Israeli founder Cilento Costa Rican founder French Canadian founder Italian founder Northern Finnish founder Romanian founder South Tyrolean Vis founder Split founder Population for which insufficient information is available to allocate it to a specific ancestral group or which contain individuals from a range of known ancestry categories, eg American undefined ancestry population African Caribbean Afro-Caribbean African American Talana Pima Indian Plains American Indian Kosraen Native Hawaiian Pacific Islander Yoruban West African Dai Chinese Hui Chinese Jingpo Chinese Malaysian Chinese Uigur Chinese Uygur Chinese Tibetan Han Taiwanese Taiwanese Han Sri Lankan Sinhalese Tatar Bashkir Includes individuals who either self-report or have been described by authors as Aboriginal Australian of Martu ancestry. The Martu Australian Aboriginal people are from the Western Desert region located across the Pilbara in Western Australia Mardu Aboriginal Australian Mardu Australian Aboriginal Martu Aboriginal Australian PMID:27070114 Martu Australian Aboriginal Jewish Israeli Punjabi Sikh American of European ancestry European American The Esan people are one of the major ethnic groups in Edo State, Nigeria who speak the Esan language. (PMID:10146569) Samples from this population were studied as part of the full 1000 Genomes project (https://www.coriell.org/1/NHGRI/Collections/1000-Genomes-Collections/Esan-in-Nigeria-ESN) Esan The Luhya are the second-largest ethnic group in Kenya and are comprised of subgroups that speak a common Bantu language. (PMID: 27813082) The Luhya ancestry group was assembled as part of phase III of the HapMap project and used in a number of rare variant density studies (PMID:22373165, PMID:26673965) Luhya The Maasai are an indigenous African ethnic group of semi-nomadic people located in northern Tanzania and Kenya. (PMID:29868928) The Maasai ancestry group was assembled as part of phase III of the HapMap project and used as reference in a range of population genetic studies (PMID:28049708). Maasai The Mende people are one of the largest ethnic groups in Sierra Leone who speak a language of the Mande branch of the Niger-Congo family. (PMID:15761855) Samples from this population were studied as part of the full 1000 Genomes project (https://www.coriell.org/1/NHGRI/Collections/1000-Genomes-Collections/Mende-in-Sierra-Leone-MSL) Mende Native people residing in the Arctic of Alaska, northern Canada, Greenland, or eastern Siberia PMID:25884279 PMID:29220501 Class previously labelled as "Eskimo", which is outdated and culturally inappropriate. Outdated label may be added as an appropriately flagged synonym at a later stage. Inuit Includes individuals with ethnic origins in the Semitic people populating the Arabian Peninsula and other countries in the Middle East and Northern Africa PMID:27393651 PMID:28106113 Arab Includes individuals who either self-report or have been described by authors as Singaporean Malay. PMID:19700652 PMID:31626772 Singaporean Malay Includes individuals who either self-report or have been described by authors as Singaporean Indian. PMID:19700652 PMID:31626772 Singaporean Indian A collective generic term that refers here to a wide variety of dependencies, areas of special sovereignty, uninhabited islands, and other entities in addition to the traditional countries or independent states. Country population PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/ PERSON: Philippe Rocca-Serra adapted from Oxford English Dictionnary rem1: collection somehow always involve a selection process population population organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization obsolete_Punjabi Sikh true true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts true GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' involved in BP If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).