http://purl.obolibrary.org/obo/ExO_0000002 ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology). Environment Exposure Ontology 2023-02-14 definition definition textual definition A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> DEFINITION definition definition textual definition A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. NCI DEFINITION PT NCI editor note IAO:0000700 uberon has_ontology_root_term true has_ontology_root_term has ontology root term preferred_root term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg term replaced by 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 medically relevant exposure uberon dc-description true dc-description description uberon dc-title true dc-title title uberon dcterms-license true dcterms-license license subset property subset_property A property representing a reference to an identical or very similar object in another database. Conceptual Entity xRef database_cross_reference xRef A property representing a reference to an identical or very similar object in another database. NCI http://www.geneontology.org/page/ontology-structure A property representing a fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. FULL_SYN Synonym with Source Data has exact synonym has_exact_synonym A property representing a fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. NCI FULL_SYN PT NCI Synonym with Source Data SY NCI label label label 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) For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) 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/ 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 https://code.google.com/p/obo-relations/wiki/ROAndTime 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 BFO:0000050 experimental_condition_ontology external quality source spatial uberon part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) PMID:15892874 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) Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. 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/ 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 https://code.google.com/p/obo-relations/wiki/ROAndTime 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 BFO:0000051 chebi_ontology external quality source spatial uberon has_part false has_part We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. has part has part has_part Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. PATOC:CJM realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes preceded by X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) 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 BFO:0000062 is preceded by takes place after external uberon preceded_by preceded_by preceded by preceded by preceded_by is preceded by SIO:000249 takes place after Allen:precedes 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. BFO:0000063 external uberon precedes precedes precedes precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. BSPO:0000120 spatial uberon in_left_side_of in_left_side_of in left side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. BSPO:PATO_mtg_2009 X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion. BSPO:0000121 spatial uberon in_right_side_of in_right_side_of in right side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion. BSPO:PATO_mtg_2009 X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure BSPO:0000126 spatial uberon in_lateral_side_of in_lateral_side_of in lateral side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure UBERON:cjm A duck swimming in a pond is partially surrounded by air and partially surrounded by water. x partially_surrounded_by y if and only if (1) x is adjacent to y and for the region r that is adjacent to x, r partially overlaps y (2) the shared boundary between x and y occupies a non-trivial proportion of the outermost boundary of x Definition modified from 'surrounded by'. partially_surrounded_by A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity. derives from part of To be ceded to RO results in proliferation of A relation between a process and a disposition such that the existence of the disposition is caused by the execution of the process. Consider ceding to RO 2018-11-03T20:58:13Z generates has food substance analog A defining ingredient defines what a food is principally categorized as, rather than an ingredient listed by percentage of weight or volume. A food may have more than one defining ingredient. Damion Dooley FoodOn For example, 'bean soup' has a defining ingredient of some 'bean (whole)'. Similarly, spicy chicken wings require a defining ingredient of (usually minute) amounts of chilli. A soup may 'has ingredient' some bean, but that doesn't make it a 'bean soup', i.e. there should be no inference to that category. However, some classes may have that simple ingredient "necessary and sufficient" equivalency. has defining ingredient A relation attaching between a food material and another food material that has been added to it at some point in its history. Damion Dooley FoodOn has ingredient has country of origin hasCountryOfOrigin has_specified_input has_specified_input The inverse property of is_specified_input_of has_specified_input has_specified_output has_specified_output The inverse property of is_specified_output_of has_specified_output inheres in this fragility inheres in this vase this fragility is a characteristic of this vase this red color inheres in this apple 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. a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in RO:0000052 characteristic_of 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 inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence 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 RO:0000053 external uberon bearer_of bearer_of has_characteristic bearer of 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 RO:0000056 external uberon participates_in participates_in participates in 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 RO:0000057 external has_participant has_participant has participant 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 RO:0000079 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 RO:0000080 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 RO:0000081 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 RO:0000085 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 RO:0000086 uberon has_quality has_quality 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 RO:0000087 chebi_ontology has_role false false has_role 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 RO:0000091 has_disposition has disposition inverse of has disposition RO:0000092 disposition_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. disposition of this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into 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 contains 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 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. X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 David Osumi-Sutherland A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of 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. dos 2017-05-24T09:30:46Z RO:0002013 external has_regulatory_component_activity has_regulatory_component_activity 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. dos 2017-05-24T09:31:01Z RO:0002014 external has_negative_regulatory_component_activity has_negative_regulatory_component_activity 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. dos 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity 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 dos 2017-05-24T09:44:33Z RO:0002017 has_component_activity 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. dos 2017-05-24T09:49:21Z RO:0002018 has_component_process has component process dos 2017-09-17T13:52:24Z RO:0002022 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. 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. GOC:dos 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. dos 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by 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. GOC:dos 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. dos 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by 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. GOC:dos 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. dos 2017-09-22T14:14:36Z RO:0002025 has_effector_activity 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. GOC:dos David Osumi-Sutherland 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. during which ends David Osumi-Sutherland RO:0002086 ends_after X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) David Osumi-Sutherland starts_at_end_of A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of external uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately preceded by immediately_preceded_by A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. SIO:000251 is immediately preceded by SIO:000251 David Osumi-Sutherland 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. during which starts David Osumi-Sutherland ends_at_start_of meets RO:0002090 external immediately_precedes immediately_precedes X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes immediately precedes David Osumi-Sutherland io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during David Osumi-Sutherland o overlaps X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during x overlaps y if and only if there exists some z such that x has part z and z part of y x overlaps y iff they have some part in common. http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 external spatial uberon overlaps overlaps "(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF [] overlaps overlaps true x overlaps y iff they have some part in common. BSPO:cjm X continuous_with Y if and only if X and Y share a fiat boundary. David Osumi-Sutherland connected to The label for this relation was previously connected to. I relabeled this to "continuous with". 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) continuous with FMA:85972 lactation SubClassOf 'only in taxon' some 'Mammalia' x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria Chris Mungall RO:0002160 uberon only_in_taxon only_in_taxon only in taxon x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. Chris Mungall Jennifer Deegan RO:0002162 uberon in_taxon in_taxon Connects a biological entity to its taxon of origin. in taxon A is spatially_disjoint_from B if and only if they have no parts in common 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. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern The M8 connects Glasgow and Edinburgh a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern 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. RO:0002180 external uberon has_component has_component has component has component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan This is the transitive form of the develops from relation develops from develops from develops_from inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan develops into Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. Chris Mungall David Osumi-Sutherland has developmental precursor FBbt TODO - add child relations from DOS directly develops from inverse of directly develops from developmental precursor of directly develops into 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. process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 external regulates regulates regulates regulates regulates (processual) Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) RO:0002212 external negatively_regulates negatively_regulates negatively regulates negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) RO:0002213 external positively_regulates positively_regulates positively regulates 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. Chris Mungall 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)". RO_0000053 some (RO_0000054 only ?Y) RO:0002215 external uberon capable_of capable_of capable of 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. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) RO:0002216 external uberon capable_of_part_of capable_of_part_of capable of part of capable of part of true x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x Chris Mungall surrounded by surrounded by A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO Chris Mungall adjacent to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. inverse of surrounded by Chris Mungall surrounds Chris Mungall 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 RO:0002222 temporally_related_to A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to inverse of starts with Chris Mungall Allen RO:0002223 uberon starts starts starts starts 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. Chris Mungall started by RO:0002224 external uberon starts_with starts_with starts with starts with x develops from part of y if and only if there exists some z such that x develops from z and z is part of y Chris Mungall develops from part of x develops_in y if x is located in y whilst x is developing Chris Mungall EHDAA2 Jonathan Bard, EHDAA2 develops in inverse of ends with Chris Mungall RO:0002229 uberon ends ends ends ends 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. Chris Mungall finished by RO:0002230 external uberon ends_with ends_with ends with ends with x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y Chris Mungall ends with process that occurs in has end location 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. Chris Mungall consumes RO:0002233 external has_input has_input has input has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. Chris Mungall produces RO:0002234 external has_output has_output has output has output A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor ExO:0000055 has exposure route A broad relationship between an exposure event or process and the course takes from the source to the target. http://purl.obolibrary.org/obo/ExO_0000004 has exposure transport path Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. related via exposure to Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y Chris Mungall has developmental contribution from inverse of has developmental contribution from Chris Mungall developmentally contributes to Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by 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. RO:0002263 acts_upstream_of 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. RO:0002264 affects acts_upstream_of_or_within acts upstream of or within Inverse of developmentally preceded by Chris Mungall developmentally succeeded by 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue Chris Mungall part of developmental precursor of p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. Chris Mungall RO:0002295 external results_in_developmental_progression_of results_in_developmental_progression_of results in developmental progression of results in developmental progression of an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) Chris Mungall GOC:mtg_berkeley_2013 RO:0002297 external results_in_formation_of results_in_formation_of results in formation of results in formation of Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. Pier Buttigieg adapted for living in A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. has habitat has habitat 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. cjm RO:0002304 external causally_upstream_of,_positive_effect causally_upstream_of,_positive_effect 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. cjm RO:0002305 external causally_upstream_of,_negative_effect causally_upstream_of,_negative_effect holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. Austin Meier Chris Mungall Marie Angelique Laporte cjm 2017-06-05T17:35:04Z has exposure stimulus 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. q inheres in 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 Because part_of is transitive, inheres in is a sub-relation of inheres in part of Chris Mungall inheres in part of RO:0002314 characteristic_of_part_of characteristic of part of inheres in part of true A relationship that holds via some environmental process Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. RO:0002320 evolutionarily_related_to evolutionarily related to A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions ecologically related to A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships RO:0002323 mereotopologically_related_to mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development RO:0002324 developmentally_related_to developmentally 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. Chris Mungall 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. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. RO:0002327 enables enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 uberon functionally_related_to functionally_related_to functionally related to functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false RO:0002329 part_of_structure_that_is_capable_of 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 Chris Mungall actively involved in enables part of RO:0002331 involved_in involved in inverse of enables Chris Mungall RO:0002333 enabled_by enabled by inverse of regulates Chris Mungall regulated by (processual) RO:0002334 external regulated_by regulated_by regulated by regulated by inverse of negatively regulates Chris Mungall RO:0002335 external negatively_regulated_by negatively_regulated_by negatively regulated by negatively regulated by inverse of positively regulates Chris Mungall RO:0002336 external positively_regulated_by positively_regulated_by positively regulated by positively regulated by An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member inverse of has input Chris Mungall RO:0002352 uberon input_of input_of input of input of inverse of has output Chris Mungall RO:0002353 external uberon output_of output_of output of output of Chris Mungall RO:0002354 formed_as_result_of formed as result of A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location Chris Mungall This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y Chris Mungall has potential to developmentally contribute to x has the potential to develop into y iff x develops into y or if x is capable of developing into y Chris Mungall has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y Chris Mungall has potential to directly develop into inverse of upstream of Chris Mungall RO:0002404 external causally_downstream_of causally_downstream_of causally downstream of causally downstream of Chris Mungall RO:0002405 external immediately_causally_downstream_of immediately_causally_downstream_of immediately 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. Chris Mungall indirectly activates RO:0002407 indirectly_positively_regulates indirectly positively regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall indirectly inhibits RO:0002409 indirectly_negatively_regulates indirectly negatively regulates This relation groups causal relations between material entities and causal relations between processes 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. 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. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to 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 if and only if p precedes q and p and q are linked in a causal chain 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. Chris Mungall RO:0002411 external causally_upstream_of causally_upstream_of causally upstream of causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. 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. Chris Mungall RO:0002412 external immediately_causally_upstream_of immediately_causally_upstream_of immediately causally upstream of immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. 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 Chris Mungall influences (processual) RO:0002418 external affects causally_upstream_of_or_within causally_upstream_of_or_within causally upstream of or within inverse of causally upstream of or within Chris Mungall RO:0002427 external causally_downstream_of_or_within causally_downstream_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 Chris Mungall RO:0002428 involved_in_regulation_of involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall RO:0002429 involved_in_positive_regulation_of involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall RO:0002430 involved_in_negative_regulation_of 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 Chris Mungall involved in or reguates RO:0002431 involved_in_or_involved_in_regulation_of involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in is active in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' 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. Chris Mungall 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. RO:0002434 in pairwise interaction with source interacts_with interacts_with interacts with http://purl.obolibrary.org/obo/MI_0914 http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations 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. Chris Mungall binds molecularly binds with RO:0002436 molecularly_interacts_with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. RO:0002447 phosphorylates 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. Chris Mungall Vasundra Touré RO:0002448 molecularly controls directly_regulates_activity_of 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. Chris Mungall Vasundra Touré directly inhibits RO:0002449 molecularly decreases activity of directly_negatively_regulates_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. Chris Mungall Vasundra Touré directly activates RO:0002450 molecularly increases activity of directly_positively_regulates_activity_of directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. RO:0002464 helper_property_(not_for_use_in_curation) helper property (not for use in curation) 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. Chris Mungall composed primarily of p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true Chris Mungall RO:0002481 is_kinase_activity is kinase activity x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships Chris Mungall transformation of x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t Chris Mungall immediate transformation of A relationship between a material entity and a process where the material entity has some causal role that influences the process RO:0002500 causal_agent_in_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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. 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. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002501 causal_relation_between_processes causal relation between processes Chris Mungall RO:0002502 depends_on 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 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002506 causal_relation_between_entities causal relation between entities A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future Chris Mungall determined by (system to material entity) Chris Mungall Pier Buttigieg determined by inverse of determined by Chris Mungall determines (material entity to system) determines s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. Chris Mungall determined by part of true Chris Mungall causally influenced by (entity-centric) RO:0002559 causally_influenced_by causally influenced by Chris Mungall RO:0002563 interaction_relation_helper_property interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall RO:0002564 molecular_interaction_relation_helper_property 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). Chris Mungall Vasundra Touré causally influences (entity-centric) RO:0002566 causally_influences causally influences Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) RO:0002578 directly_regulates 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 Chris Mungall RO:0002584 has_part_structure_that_is_capable_of has part structure that is capable of p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p RO:0002586 results_in_breakdown_of results in breakdown of RO:0002588 external results_in_assembly_of results_in_assembly_of results in assembly of RO:0002590 external results_in_disassembly_of results_in_disassembly_of results in disassembly of p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 external results_in_organization_of results_in_organization_of results in organization 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. Chris Mungall RO:0002595 causal_relation_between_material_entity_and_a_process 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. RO:0002596 capable_of_regulating capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. RO:0002597 capable_of_negatively_regulating 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. RO:0002598 capable_of_positively_regulating capable of positively regulating Inverse of 'causal agent in process' RO:0002608 external process_has_causal_agent process_has_causal_agent process has causal agent Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) RO:0002629 directly_positively_regulates directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) RO:0002630 directly_negatively_regulates directly negatively regulates a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel produced by p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. cjm 2018-12-13T11:26:17Z RO:0004007 external has_primary_input_or_output has_primary_input_or_output has primary input or output p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. cjm 2018-12-13T11:26:32Z RO:0004008 external has_primary_output has_primary_output has primary output p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. GOC:cjm GOC:dph GOC:kva GOC:pt PMID:27812932 A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. cjm 2017-12-26T19:45:49Z realized in response to stimulus Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z RO:0004031 enables_subfunction enables subfunction cjm 2018-01-26T23:49:30Z RO:0004032 acts_upstream_of_or_within,_positive_effect acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z RO:0004033 acts_upstream_of_or_within,_negative_effect 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 cjm 2018-01-26T23:53:14Z RO:0004034 acts_upstream_of,_positive_effect 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 cjm 2018-01-26T23:53:22Z RO:0004035 acts_upstream_of,_negative_effect acts upstream of, negative effect cjm 2018-03-13T23:55:05Z RO:0004046 causally_upstream_of_or_within,_negative_effect causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z RO:0004047 causally_upstream_of_or_within,_positive_effect causally upstream of or within, positive effect "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. Damion Dooley has substance added A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. Austin Meier Chris Mungall David Osumi-Sutherland Marie Angelique Laporte triggered by process realized in response to https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit triggered by process RO:cjm 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. Vasundra Touré RO:0011002 regulates_activity_of 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. pg 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. pg 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates indirectly regulates q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. different in magnitude relative to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased in magnitude relative to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased in magnitude relative to q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. reciprocal of q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. https://orcid.org/0000-0002-6601-2165 X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 2021-12-14T20:41:45Z has exposure medium 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. https://orcid.org/0000-0001-9625-1899 https://orcid.org/0000-0003-2620-0345 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 RO:0017001 device_utilizes_material 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. RO:0019000 gene_ontology regulates_characteristic regulates_characteristic 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. RO:0019001 gene_ontology positively_regulates_characteristic positively_regulates_characteristic 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. RO:0019002 gene_ontology negatively_regulates_characteristic negatively_regulates_characteristic negatively regulates characteristic p has anatomical participant c iff p has participant c, and c is an anatomical entity cjm 2018-09-26T01:08:58Z RO:0040036 external results_in_changes_to_anatomical_or_cellular_structure results_in_changes_to_anatomical_or_cellular_structure results in changes to anatomical or cellular structure chebi_ontology has_functional_parent false false has functional parent chebi_ontology has_parent_hydride false false has parent hydride chebi_ontology is_conjugate_acid_of true false is conjugate acid of chebi_ontology is_conjugate_base_of true false is conjugate base of chebi_ontology is_enantiomer_of true false is enantiomer of chebi_ontology is_substituent_group_from false false is substituent group from source interacts_with_an_exposure_receptor_via interacts_with_an_exposure_receptor_via source interacts_with_an_exposure_stressor_via interacts_with_an_exposure stressor_via has_participant q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality decreased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased_in_magnitude_relative_to q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality different_in_magnitude_relative_to different_in_magnitude_relative_to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality increased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased_in_magnitude_relative_to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. quality reciprocal_of There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. reciprocal_of q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. PATOC:CJM 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 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 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. 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 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] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] 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 A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. 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]) 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] independent continuant 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 t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. 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]) 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]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] source BFO:0000015 process process 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]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet 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. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] 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 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 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. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) 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] 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] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role 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. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] object aggregate site object gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] material MaterialEntity material entity material entity 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] bfo BFO:0000040 material entity 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] b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) immaterial entity Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. spatial CARO:0000000 anatomical entity anatomical entity Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. CARO:MAH Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. spatial CARO:0000003 anatomical structure connected anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CC:DOS An anatomical entity that has mass. spatial CARO:0000006 material anatomical entity material anatomical entity An anatomical entity that has mass. CC:DOS organism or virus or viroid biological entity A material entity that is ingested and contributes to survival, growth and development dietary chemical component Carbohydrates that are absorbed in the small intestine and provide carbohydrate for metabolism in monogastric animals. digestible carbohydrate available carbohydrate Available carbohydrate in monosaccharide and disaccharide form free sugar A carbohydrate that resists enzymatic digestion in the digestive systems of humans and other monogastric species. dietary fibre Dietary fibre which dissolves in water and is primarily fermented in the colon of monogastric animals by gut bacteria soluble dietary fibre Dietary fibre which does not dissolve in water and is inert to digestive enzymes in the upper gastrointestinal tract of monogastric animals. insoluble dietary fibre A mineral nutrient that represents a major proportion of the minerals required in the diet macromineral macro element Mineral nutrient that is present in a very low concentration within the diet micromineral trace element A plant metabolite that is not essential for growth or division of plant cells. secondary metabolite plant secondary metabolite An organic molecule that has a vitamin(role) This term can be assigned to CHEBI or any other ontology that claims it vitamin (molecular entity) Calcium ingested by an organism that contributes to the survival, growth, development, or other biological function of itself, its bionts, or its holobionts dietary calcium Chlorine ingested by an organism that contributes to the survival, growth, development, or other biological function of itself, its bionts, or its holobionts dietary chlorine Magnesium ingested by an organism that contributes to the survival, growth, development, or other biological function of itself, its bionts, or its holobionts dietary magnesium Phosphorus ingested by an organism that contributes to the survival, growth, development, or other biological function of itself, its bionts, or its holobionts dietary phosphorus Potassium ingested by an organism that contributes to the survival, growth, development, or other biological function of itself, its bionts, or its holobionts dietary potassium Sodium ingested by an organism that contributes to the survival, growth, development, or other biological function of itself, its bionts, or its holobionts dietary sodium Sulfur ingested by an organism that contributes to the survival, growth, development, or other biological function of itself, its bionts, or its holobionts dietary sulfur Copper ingested by an organism that contributes to the survival, growth, development, or other biological function of itself, its bionts, or its holobionts dietary copper Fluorine ingested by an organism that contributes to the survival, growth, development, or other biological function of itself, its bionts, or its holobionts dietary fluorine Iron ingested by an organism that contributes to the survival, growth, development, or other biological function of itself, its bionts, or its holobionts dietary iron A complex carbohydrate with various rheological properties that result in viscoelastic behavior gum Glucose which is derived from sucrose. glucose derived from sucrose Fructose which is derived from sucrose. fructose derived from sucrose Glucose which is derived from maltose. glucose derived from maltose Raffinose which is derived from raffinose family oligosaccharide. raffinose derived from raffinose family oligosaccharide Glucose which is derived from raffinose derived from raffinose family oligosaccharide. glucose derived from raffinose derived from raffinose family oligosaccharide Fructose which is derived from raffinose derived from raffinose family oligosaccharide. fructose derived from raffinose derived from raffinose family oligosaccharide Inulin which is derived from fructan. inulin derived from fructan Fructose which is derived from inulin derived from fructan. fructose derived from inulin derived from fructan Amino acid which is derived from protein. amino acid derived from protein The concentration of dietary chemical component when measured in some material entity. material entity dietary chemical component concentration concentration of dietary chemical component in material entity The concentration of water when measured in some material entity. INFOODs:WATER USDA_NDB:1051 material entity water concentration concentration of water in material entity The concentration of carbohydrate when measured in some material entity. USDA_NDB:1005 USDA_NDB:1050 USDA_NDB:1072 material entity carbohydrate concentration concentration of carbohydrate in material entity The concentration of polysaccharide when measured in some material entity. INFOODs:POLYSAC material entity polysaccharide concentration concentration of polysaccharide in material entity The concentration of inulin when measured in some material entity. INFOODs:INULN USDA_NDB:1403 material entity inulin concentration concentration of inulin in material entity The concentration of monosaccharide when measured in some material entity. INFOODs:MNSAC material entity monosaccharide concentration concentration of monosaccharide in material entity The concentration of glucose when measured in some material entity. INFOODs:GLUFB INFOODs:GLUS USDA_NDB:1011 material entity glucose concentration concentration of glucose in material entity The concentration of fructose when measured in some material entity. INFOODs:FRUFB INFOODs:FRUS USDA_NDB:1012 material entity fructose concentration concentration of fructose in material entity The concentration of rhamnose when measured in some material entity. INFOODs:RHAFB INFOODs:RHAS material entity rhamnose concentration concentration of rhamnose in material entity The concentration of disaccharide when measured in some material entity. INFOODs:DISAC material entity disaccharide concentration concentration of disaccharide in material entity The concentration of sucrose when measured in some material entity. INFOODs:SUCS USDA_NDB:1010 material entity sucrose concentration concentration of sucrose in material entity The concentration of trehalose when measured in some material entity. INFOODs:TRES material entity trehalose concentration concentration of trehalose in material entity The concentration of maltose when measured in some material entity. INFOODs:MALS USDA_NDB:1014 material entity maltose concentration concentration of maltose in material entity The concentration of oligosaccharide when measured in some material entity. INFOODs:OLSAC INFOODs:OLSACM material entity oligosaccharide concentration concentration of oligosaccharide in material entity The concentration of raffinose family oligosaccharide when measured in some material entity. INFOODs:RAFS material entity raffinose family oligosaccharide concentration concentration of raffinose family oligosaccharide in material entity The concentration of raffinose when measured in some material entity. INFOODs:RAFS material entity raffinose concentration concentration of raffinose in material entity The concentration of available carbohydrate when measured in some material entity. INFOODs:CHOAVL INFOODs:CHOAVL- INFOODs:CHOAVLDF INFOODs:CHOAVLM INFOODs:CHOAVLO USDA_NDB:1005 material entity available carbohydrate concentration concentration of available carbohydrate in material entity The concentration of free sugar when measured in some material entity. INFOODs:SUGAR INFOODs:SUGAR- INFOODs:SUGARM USDA_NDB:1063 USDA_NDB:1235 USDA_NDB:2000 material entity free sugar concentration concentration of free sugar in material entity The concentration of dietary fibre when measured in some material entity. INFOODs:FIB- INFOODs:FIBC INFOODs:FIBDF INFOODs:FIBTGLC USDA_NDB:2033 material entity dietary fibre concentration concentration of dietary fibre in material entity The concentration of soluble dietary fibre when measured in some material entity. INFOODs:FIBGLCSSOL INFOODs:PSACNSS USDA_NDB:1082 material entity soluble dietary fibre concentration concentration of soluble dietary fibre in material entity The concentration of insoluble dietary fibre when measured in some material entity. INFOODs:FIBC INFOODs:FIBGLCSINS INFOODs:FIBGLCSINSOL INFOODs:FIBINS INFOODs:FIBTGLCS USDA_NDB:1084 material entity insoluble dietary fibre concentration concentration of insoluble dietary fibre in material entity The concentration of fructan when measured in some material entity. INFOODs:FRUTN INFOODs:FRUTNM material entity fructan concentration concentration of fructan in material entity The concentration of protein when measured in some material entity. INFOODs:PROT- USDA_NDB:1003 material entity protein concentration concentration of protein in material entity The concentration of cysteine when measured in some material entity. INFOODs:CYSTE USDA_NDB:1232 material entity cysteine concentration concentration of cysteine in material entity The concentration of histidine when measured in some material entity. INFOODs:HIS USDA_NDB:1221 material entity histidine concentration concentration of histidine in material entity The concentration of leucine when measured in some material entity. INFOODs:LEU USDA_NDB:1213 material entity leucine concentration concentration of leucine in material entity The concentration of methionine when measured in some material entity. INFOODs:MET USDA_NDB:1215 material entity methionine concentration concentration of methionine in material entity The concentration of phenylalanine when measured in some material entity. INFOODs:PHE USDA_NDB:1217 material entity phenylalanine concentration concentration of phenylalanine in material entity The concentration of proline when measured in some material entity. INFOODs:PRO USDA_NDB:1226 material entity proline concentration concentration of proline in material entity The concentration of lipid when measured in some material entity. INFOODs:FATPL USDA_NDB:1004 material entity lipid concentration concentration of lipid in material entity The concentration of propionic acid when measured in some material entity. INFOODs:PROPAC material entity propionic acid concentration concentration of propionic acid in material entity The concentration of palmitoleic acid when measured in some material entity. material entity palmitoleic acid concentration concentration of palmitoleic acid in material entity The concentration of ω−3 fatty acid when measured in some material entity. material entity ω−3 fatty acid concentration concentration of ω−3 fatty acid in material entity The concentration of ω−6 fatty acid when measured in some material entity. material entity ω−6 fatty acid concentration concentration of ω−6 fatty acid in material entity The concentration of arachidonic acid when measured in some material entity. material entity arachidonic acid concentration concentration of arachidonic acid in material entity The concentration of sterol when measured in some material entity. INFOODs:STEOTH INFOODs:STERFRE INFOODs:STERT material entity sterol concentration concentration of sterol in material entity The concentration of cholesterol when measured in some material entity. INFOODs:CHOLEST USDA_NDB:1253 material entity cholesterol concentration concentration of cholesterol in material entity The concentration of mineral nutrient when measured in some material entity. material entity mineral nutrient concentration concentration of mineral nutrient in material entity The concentration of macro element when measured in some material entity. material entity macro element concentration concentration of macro element in material entity The concentration of chloride when measured in some material entity. INFOODs:CLD material entity chloride concentration concentration of chloride in material entity The concentration of potassium(1+) when measured in some material entity. INFOODs:K USDA_NDB:1092 material entity potassium(1+) concentration concentration of potassium(1+) in material entity The concentration of trace element when measured in some material entity. material entity trace element concentration concentration of trace element in material entity The concentration of copper(2+) when measured in some material entity. INFOODs:CU USDA_NDB:1098 material entity copper(2+) concentration concentration of copper(2+) in material entity The concentration of fluoride when measured in some material entity. INFOODs:FD USDA_NDB:1099 material entity fluoride concentration concentration of fluoride in material entity The concentration of iron(2+) when measured in some material entity. INFOODs:FE USDA_NDB:1089 material entity iron(2+) concentration concentration of iron(2+) in material entity The concentration of lithium(1+) when measured in some material entity. INFOODs:LI material entity lithium(1+) concentration concentration of lithium(1+) in material entity The concentration of salt when measured in some material entity. INFOODs:NACL material entity salt concentration concentration of salt in material entity The concentration of sodium chloride when measured in some material entity. material entity sodium chloride concentration concentration of sodium chloride in material entity The concentration of vitamin (molecular entity) when measured in some material entity. material entity vitamin (molecular entity) concentration concentration of vitamin (molecular entity) in material entity The concentration of B vitamin when measured in some material entity. material entity B vitamin concentration concentration of B vitamin in material entity The concentration of vitamin B1 when measured in some material entity. INFOODs:THIA- USDA_NDB:1165 material entity vitamin B1 concentration concentration of vitamin B1 in material entity The concentration of riboflavin when measured in some material entity. INFOODs:RIBF USDA_NDB:1166 material entity riboflavin concentration concentration of riboflavin in material entity The concentration of nicotinic acid when measured in some material entity. INFOODs:NIA- USDA_NDB:1167 material entity nicotinic acid concentration concentration of nicotinic acid in material entity The concentration of biotin when measured in some material entity. INFOODs:BIOT USDA_NDB:1176 material entity biotin concentration concentration of biotin in material entity The concentration of folic acid when measured in some material entity. INFOODs:FOLAC USDA_NDB:1186 material entity folic acid concentration concentration of folic acid in material entity The concentration of vitamin C when measured in some material entity. INFOODs:VITC INFOODs:VITC- USDA_NDB:1162 material entity vitamin C concentration concentration of vitamin C in material entity The concentration of L-ascorbic acid when measured in some material entity. INFOODs:ASCL material entity L-ascorbic acid concentration concentration of L-ascorbic acid in material entity The concentration of vitamin A when measured in some material entity. INFOODs:VITA INFOODs:VITA- INFOODs:VITAA USDA_NDB:1104 USDA_NDB:1106 material entity vitamin A concentration concentration of vitamin A in material entity The concentration of carotenoid when measured in some material entity. INFOODs:CARTOID material entity carotenoid concentration concentration of carotenoid in material entity The concentration of β-carotene when measured in some material entity. INFOODs:CARTB USDA_NDB:1107 material entity β-carotene concentration concentration of β-carotene in material entity The concentration of vitamin D when measured in some material entity. INFOODs:VITD INFOODs:VITD- USDA_NDB:1110 material entity vitamin D concentration concentration of vitamin D in material entity The concentration of vitamin E when measured in some material entity. INFOODs:VITE INFOODs:VITE- INFOODs:VITEA USDA_NDB:1124 USDA_NDB:1158 USDA_NDB:1242 material entity vitamin E concentration concentration of vitamin E in material entity The concentration of tocopherol when measured in some material entity. INFOODs:TOCPHT material entity tocopherol concentration concentration of tocopherol in material entity The concentration of α-tocopherol when measured in some material entity. INFOODs:TOCPHA USDA_NDB:1109 material entity α-tocopherol concentration concentration of α-tocopherol in material entity The concentration of vitamin K when measured in some material entity. INFOODs:VITK material entity vitamin K concentration concentration of vitamin K in material entity The concentration of plant secondary metabolite when measured in some material entity. material entity plant secondary metabolite concentration concentration of plant secondary metabolite in material entity The concentration of alkaloid when measured in some material entity. material entity alkaloid concentration concentration of alkaloid in material entity The concentration of caffeine when measured in some material entity. INFOODs:CAFFN USDA_NDB:1057 material entity caffeine concentration concentration of caffeine in material entity The concentration of phenols when measured in some material entity. material entity phenols concentration concentration of phenols in material entity The concentration of polyphenol when measured in some material entity. INFOODs:POLYPHENT material entity polyphenol concentration concentration of polyphenol in material entity The concentration of tannin when measured in some material entity. INFOODs:TAN material entity tannin concentration concentration of tannin in material entity The concentration of catechol when measured in some material entity. material entity catechol concentration concentration of catechol in material entity The concentration of phenolic acid when measured in some material entity. material entity phenolic acid concentration concentration of phenolic acid in material entity The concentration of hydroxybenzoic acid when measured in some material entity. material entity hydroxybenzoic acid concentration concentration of hydroxybenzoic acid in material entity The concentration of salicylic acid when measured in some material entity. INFOODs:SALAC material entity salicylic acid concentration concentration of salicylic acid in material entity The concentration of methyl ketone when measured in some material entity. material entity methyl ketone concentration concentration of methyl ketone in material entity The concentration of acetophenone when measured in some material entity. material entity acetophenone concentration concentration of acetophenone in material entity The concentration of naphthoquinone when measured in some material entity. material entity naphthoquinone concentration concentration of naphthoquinone in material entity The concentration of 1,4-napthoquinone when measured in some material entity. material entity 1,4-napthoquinone concentration concentration of 1,4-napthoquinone in material entity The concentration of stilbenoid when measured in some material entity. material entity stilbenoid concentration concentration of stilbenoid in material entity The concentration of stilbene when measured in some material entity. material entity stilbene concentration concentration of stilbene in material entity The concentration of flavonoids when measured in some material entity. INFOODs:FLAVD material entity flavonoids concentration concentration of flavonoids in material entity The concentration of flavonoid when measured in some material entity. INFOODs:FLAVD material entity flavonoid concentration concentration of flavonoid in material entity The concentration of flavan when measured in some material entity. material entity flavan concentration concentration of flavan in material entity The concentration of flavanone when measured in some material entity. material entity flavanone concentration concentration of flavanone in material entity The concentration of naringenin when measured in some material entity. INFOODs:NARING material entity naringenin concentration concentration of naringenin in material entity The concentration of flavone when measured in some material entity. material entity flavone concentration concentration of flavone in material entity The concentration of chrysin when measured in some material entity. material entity chrysin concentration concentration of chrysin in material entity The concentration of quercetin when measured in some material entity. INFOODs:QUERCE material entity quercetin concentration concentration of quercetin in material entity The concentration of hydroxyflavan when measured in some material entity. material entity hydroxyflavan concentration concentration of hydroxyflavan in material entity The concentration of catechin when measured in some material entity. INFOODs:CATEC INFOODs:CATECT material entity catechin concentration concentration of catechin in material entity The concentration of isoflavonoid when measured in some material entity. INFOODs:ISOFLVND material entity isoflavonoid concentration concentration of isoflavonoid in material entity The concentration of isoflavones when measured in some material entity. material entity isoflavones concentration concentration of isoflavones in material entity The concentration of hydroxyisoflavone when measured in some material entity. material entity hydroxyisoflavone concentration concentration of hydroxyisoflavone in material entity The concentration of daidzein when measured in some material entity. INFOODs:DDZEIN material entity daidzein concentration concentration of daidzein in material entity The concentration of genistein when measured in some material entity. INFOODs:GNSTEIN material entity genistein concentration concentration of genistein in material entity The concentration of glucoside when measured in some material entity. material entity glucoside concentration concentration of glucoside in material entity The concentration of phenylpropanoid when measured in some material entity. material entity phenylpropanoid concentration concentration of phenylpropanoid in material entity The concentration of terpenoid when measured in some material entity. material entity terpenoid concentration concentration of terpenoid in material entity The concentration of diterpenoid when measured in some material entity. material entity diterpenoid concentration concentration of diterpenoid in material entity The concentration of lycopene when measured in some material entity. INFOODs:LYCPN USDA_NDB:1122 material entity lycopene concentration concentration of lycopene in material entity The concentration of triterpenoid when measured in some material entity. material entity triterpenoid concentration concentration of triterpenoid in material entity The concentration of organic acid when measured in some material entity. INFOODs:OA material entity organic acid concentration concentration of organic acid in material entity The concentration of acetic acid when measured in some material entity. INFOODs:ACEAC USDA_NDB:1026 material entity acetic acid concentration concentration of acetic acid in material entity The concentration of ascorbic acid when measured in some material entity. material entity ascorbic acid concentration concentration of ascorbic acid in material entity The concentration of oxalic acid when measured in some material entity. INFOODs:OXALAC material entity oxalic acid concentration concentration of oxalic acid in material entity The concentration of inositol when measured in some material entity. INFOODs:INOTL USDA_NDB:1181 material entity inositol concentration concentration of inositol in material entity The concentration of polyol when measured in some material entity. INFOODs:POLYL material entity polyol concentration concentration of polyol in material entity The concentration of mannitol when measured in some material entity. INFOODs:MANTL material entity mannitol concentration concentration of mannitol in material entity The concentration of glucitol when measured in some material entity. material entity glucitol concentration concentration of glucitol in material entity The concentration of polyunsaturated fatty acid when measured in some material entity. INFOODs:FAPU INFOODs:FAPULC USDA_NDB:1293 material entity polyunsaturated fatty acid concentration concentration of polyunsaturated fatty acid in material entity The concentration of glycerol when measured in some material entity. INFOODs:GLYRL material entity glycerol concentration concentration of glycerol in material entity The concentration of triglyceride when measured in some material entity. material entity triglyceride concentration concentration of triglyceride in material entity The concentration of monounsaturated fatty acid when measured in some material entity. USDA_NDB:1292 material entity monounsaturated fatty acid concentration concentration of monounsaturated fatty acid in material entity The concentration of saturated fatty acid when measured in some material entity. INFOODs:FASAT USDA_NDB:1258 material entity saturated fatty acid concentration concentration of saturated fatty acid in material entity The concentration of amylopectin when measured in some material entity. INFOODs:AMYP material entity amylopectin concentration concentration of amylopectin in material entity The concentration of amino acid when measured in some material entity. material entity amino acid concentration concentration of amino acid in material entity The concentration of fatty acid when measured in some material entity. material entity fatty acid concentration concentration of fatty acid in material entity The concentration of glucan when measured in some material entity. material entity glucan concentration concentration of glucan in material entity The concentration of glucose derived from sucrose when measured in some material entity. INFOODs:GLUS USDA_NDB:1011 material entity glucose derived from sucrose concentration concentration of glucose derived from sucrose in material entity The concentration of fructose derived from sucrose when measured in some material entity. INFOODs:FRUS USDA_NDB:1012 material entity fructose derived from sucrose concentration concentration of fructose derived from sucrose in material entity The concentration of glucose derived from maltose when measured in some material entity. INFOODs:GLUS USDA_NDB:1011 material entity glucose derived from maltose concentration concentration of glucose derived from maltose in material entity The concentration of raffinose derived from raffinose family oligosaccharide when measured in some material entity. INFOODs:RAFS material entity raffinose derived from raffinose family oligosaccharide concentration concentration of raffinose derived from raffinose family oligosaccharide in material entity The concentration of glucose derived from raffinose derived from raffinose family oligosaccharide when measured in some material entity. INFOODs:GLUS USDA_NDB:1011 material entity glucose derived from raffinose derived from raffinose family oligosaccharide concentration concentration of glucose derived from raffinose derived from raffinose family oligosaccharide in material entity The concentration of fructose derived from raffinose derived from raffinose family oligosaccharide when measured in some material entity. INFOODs:FRUS USDA_NDB:1012 material entity fructose derived from raffinose derived from raffinose family oligosaccharide concentration concentration of fructose derived from raffinose derived from raffinose family oligosaccharide in material entity The concentration of inulin derived from fructan when measured in some material entity. INFOODs:INULN USDA_NDB:1403 material entity inulin derived from fructan concentration concentration of inulin derived from fructan in material entity The concentration of fructose derived from inulin derived from fructan when measured in some material entity. INFOODs:FRUS USDA_NDB:1012 material entity fructose derived from inulin derived from fructan concentration concentration of fructose derived from inulin derived from fructan in material entity The concentration of amino acid derived from protein when measured in some material entity. material entity amino acid derived from protein concentration concentration of amino acid derived from protein in material entity The concentration of isoprenoid when measured in some material entity. material entity isoprenoid concentration concentration of isoprenoid in material entity The concentration of terpene when measured in some material entity. material entity terpene concentration concentration of terpene in material entity The concentration of tetraterpene when measured in some material entity. material entity tetraterpene concentration concentration of tetraterpene in material entity The concentration of carotene when measured in some material entity. material entity carotene concentration concentration of carotene in material entity The concentration of tetraterpenoid when measured in some material entity. material entity tetraterpenoid concentration concentration of tetraterpenoid in material entity The concentration of methylmercury compound when measured in some material entity. material entity methylmercury compound concentration concentration of methylmercury compound in material entity The concentration of thiamine hydrochloride when measured in some material entity. INFOODs:THIAHCL material entity thiamine hydrochloride concentration concentration of thiamine hydrochloride in material entity The concentration of vitamin B2 when measured in some material entity. material entity vitamin B2 concentration concentration of vitamin B2 in material entity The concentration of vitamin B3 when measured in some material entity. material entity vitamin B3 concentration concentration of vitamin B3 in material entity The concentration of vitamin B6 when measured in some material entity. INFOODs:VITB6- USDA_NDB:1175 material entity vitamin B6 concentration concentration of vitamin B6 in material entity The concentration of vitamin B7 when measured in some material entity. material entity vitamin B7 concentration concentration of vitamin B7 in material entity The concentration of vitamin B9 when measured in some material entity. material entity vitamin B9 concentration concentration of vitamin B9 in material entity The concentration of tetrahydrofolate when measured in some material entity. INFOODs:FOLH4 material entity tetrahydrofolate concentration concentration of tetrahydrofolate in material entity The concentration of all-trans-retinol when measured in some material entity. material entity all-trans-retinol concentration concentration of all-trans-retinol in material entity The concentration of D3 vitamins when measured in some material entity. USDA_NDB:1112 material entity D3 vitamins concentration concentration of D3 vitamins in material entity The concentration of vitamin D2 when measured in some material entity. material entity vitamin D2 concentration concentration of vitamin D2 in material entity The concentration of menadione when measured in some material entity. material entity menadione concentration concentration of menadione in material entity The concentration of menaquinone when measured in some material entity. INFOODs:MK4 INFOODs:MK5 INFOODs:MK6 INFOODs:MK7 INFOODs:MK8 INFOODs:MK9 USDA_NDB:1183 material entity menaquinone concentration concentration of menaquinone in material entity The concentration of phylloquinone when measured in some material entity. USDA_NDB:1185 material entity phylloquinone concentration concentration of phylloquinone in material entity The concentration of dietary calcium when measured in some material entity. material entity dietary calcium concentration concentration of dietary calcium in material entity The concentration of inorganic calcium salt when measured in some material entity. material entity inorganic calcium salt concentration concentration of inorganic calcium salt in material entity The concentration of calcium carbonate when measured in some material entity. material entity calcium carbonate concentration concentration of calcium carbonate in material entity The concentration of calcium sulfate when measured in some material entity. material entity calcium sulfate concentration concentration of calcium sulfate in material entity The concentration of calcium hydroxide when measured in some material entity. material entity calcium hydroxide concentration concentration of calcium hydroxide in material entity The concentration of dietary chlorine when measured in some material entity. material entity dietary chlorine concentration concentration of dietary chlorine in material entity The concentration of inorganic chloride when measured in some material entity. material entity inorganic chloride concentration concentration of inorganic chloride in material entity The concentration of potassium chloride when measured in some material entity. material entity potassium chloride concentration concentration of potassium chloride in material entity The concentration of lithium chloride when measured in some material entity. material entity lithium chloride concentration concentration of lithium chloride in material entity The concentration of organic chloride salt when measured in some material entity. material entity organic chloride salt concentration concentration of organic chloride salt in material entity The concentration of organochlorine compound when measured in some material entity. material entity organochlorine compound concentration concentration of organochlorine compound in material entity The concentration of hydrogen chloride when measured in some material entity. material entity hydrogen chloride concentration concentration of hydrogen chloride in material entity The concentration of hypochlorite when measured in some material entity. material entity hypochlorite concentration concentration of hypochlorite in material entity The concentration of dietary magnesium when measured in some material entity. material entity dietary magnesium concentration concentration of dietary magnesium in material entity The concentration of inorganic magnesium salt when measured in some material entity. material entity inorganic magnesium salt concentration concentration of inorganic magnesium salt in material entity The concentration of magnesium hydroxide when measured in some material entity. material entity magnesium hydroxide concentration concentration of magnesium hydroxide in material entity The concentration of dietary phosphorus when measured in some material entity. material entity dietary phosphorus concentration concentration of dietary phosphorus in material entity The concentration of phosphoric acid when measured in some material entity. material entity phosphoric acid concentration concentration of phosphoric acid in material entity The concentration of inorganic phosphate salt when measured in some material entity. material entity inorganic phosphate salt concentration concentration of inorganic phosphate salt in material entity The concentration of sodium phosphate when measured in some material entity. material entity sodium phosphate concentration concentration of sodium phosphate in material entity The concentration of dietary potassium when measured in some material entity. material entity dietary potassium concentration concentration of dietary potassium in material entity The concentration of inorganic potassium salt when measured in some material entity. material entity inorganic potassium salt concentration concentration of inorganic potassium salt in material entity The concentration of dietary sodium when measured in some material entity. material entity dietary sodium concentration concentration of dietary sodium in material entity The concentration of inorganic sodium salt when measured in some material entity. material entity inorganic sodium salt concentration concentration of inorganic sodium salt in material entity The concentration of sodium sulfate when measured in some material entity. material entity sodium sulfate concentration concentration of sodium sulfate in material entity The concentration of sodium hydrogensulfite when measured in some material entity. material entity sodium hydrogensulfite concentration concentration of sodium hydrogensulfite in material entity The concentration of sodium fluoride when measured in some material entity. material entity sodium fluoride concentration concentration of sodium fluoride in material entity The concentration of sodium hydroxide when measured in some material entity. material entity sodium hydroxide concentration concentration of sodium hydroxide in material entity The concentration of organic sodium salt when measured in some material entity. material entity organic sodium salt concentration concentration of organic sodium salt in material entity The concentration of dietary sulfur when measured in some material entity. material entity dietary sulfur concentration concentration of dietary sulfur in material entity The concentration of inorganic sulfate salt when measured in some material entity. material entity inorganic sulfate salt concentration concentration of inorganic sulfate salt in material entity The concentration of iron(2+) sulfate (anhydrous) when measured in some material entity. material entity iron(2+) sulfate (anhydrous) concentration concentration of iron(2+) sulfate (anhydrous) in material entity The concentration of organic sulfate when measured in some material entity. material entity organic sulfate concentration concentration of organic sulfate in material entity The concentration of organosulfur compound when measured in some material entity. material entity organosulfur compound concentration concentration of organosulfur compound in material entity The concentration of glutathione when measured in some material entity. material entity glutathione concentration concentration of glutathione in material entity The concentration of dimethyl sulfoxide when measured in some material entity. material entity dimethyl sulfoxide concentration concentration of dimethyl sulfoxide in material entity The concentration of sulfur dioxide when measured in some material entity. material entity sulfur dioxide concentration concentration of sulfur dioxide in material entity The concentration of dietary copper when measured in some material entity. material entity dietary copper concentration concentration of dietary copper in material entity The concentration of dietary fluorine when measured in some material entity. material entity dietary fluorine concentration concentration of dietary fluorine in material entity The concentration of dietary iron when measured in some material entity. material entity dietary iron concentration concentration of dietary iron in material entity The concentration of inorganic iron salt when measured in some material entity. material entity inorganic iron salt concentration concentration of inorganic iron salt in material entity The concentration of gum when measured in some material entity. INFOODs:GUMS material entity gum concentration concentration of gum in material entity The concentration of carrageenan when measured in some material entity. material entity carrageenan concentration concentration of carrageenan in material entity The concentration of ketose when measured in some material entity. material entity ketose concentration concentration of ketose in material entity The concentration of ketohexose when measured in some material entity. material entity ketohexose concentration concentration of ketohexose in material entity The concentration of alditol when measured in some material entity. material entity alditol concentration concentration of alditol in material entity The concentration of curcumin when measured in some material entity. material entity curcumin concentration concentration of curcumin in material entity The concentration of stilbenol when measured in some material entity. material entity stilbenol concentration concentration of stilbenol in material entity The concentration of benzenediols when measured in some material entity. material entity benzenediols concentration concentration of benzenediols in material entity