BFO OWL specification label Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label BFO OWL specification label BFO CLIF specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label BFO CLIF specification label editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example example of usage A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> IAO:0000112 uberon example_of_usage true example_of_usage example of usage example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status definition definition textual definition 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. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition. 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. 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 The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. url:http://purl.obolibrary.org/obo/iao.owl The official definition. url:http://purl.obolibrary.org/obo/iao.owl editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note true 1 editor_note editor note editor note definition editor term editor Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor definition editor term editor term editor alternative label alternative term A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label alternative term alternative term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg IAO:0000232 uberon curator_notes true 1 curator_notes curator note curator note curator notes term tracker item term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external uberon term_tracker_item true true term_tracker_item The 'tracker item' can associate a tracker with a specific ontology term. The 'tracker item' can associate a tracker with a specific ontology term. term tracker item term tracker item imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) has associated axiom(fol) term replaced by IAO_0000125 Use on obsolete terms, relating the term to another term that can be used as a substitute Use on obsolete terms, relating the term to another term that can be used as a substitute Add as annotation triples in the granting ontology Person:Alan Ruttenberg Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. is homeomorphic for Used to capture development notes and design decisions or questions. All annotations using this property should be removed before publishing / releasing the ontology to the public (but ideally retained in some place as valuable documentation). SEPIO_editor_note an alternative term used for STATO statistical ontology and ISA team Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra STATO alternative term a R command syntax or link to a R documentation in support of Statistical Ontology Classes or Data Transformations Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra R command UNEP ignore For use in the EMBL-EBI ArrayExpress interface. has_alternative_id has_broad_synonym database_cross_reference An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. An alternative label for a given entity such as a commonly used abbreviation or synonym. Exact synonym. 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. Synonym of the term. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 FULL_SYN Synonym with Source Data has exact synonym has exact synonym has_exact_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 Exact synonym. url:http://www.geneontology.org/formats/oboInOwl#hasExactSynonym Synonym of the term. url:http://www.geneontology.org/formats/oboInOwl#hasExactSynonym has_narrow_synonym Name space of the ontology. disease_ontology has_obo_namespace Name space of the ontology. url:http://www.geneontology.org/formats/oboInOwl#hasOBONamespace has_related_synonym An identifier for an individual entity. An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. id An identifier for an individual entity. url:http://purl.obolibrary.org/obo/IAO_0020000 An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. url:http://purl.obolibrary.org/obo/IAO_0020000 in_subset shorthand Comment. comment comment Comment. url:http://www.w3.org/2000/01/rdf-schema#comment is defined by is defined by This is an experimental annotation label A human readable name for this class. A human-readable name for the subject. label label A human readable name for this class. url:http://www.w3.org/2000/01/rdf-schema#label url:https://www.w3.org/TR/owl-guide/ A human readable name for this class. url:http://www.w3.org/2000/01/rdf-schema#label http://www.w3.org/2000/01/rdf-schema#seeAlso spatial uberon seeAlso true seeAlso see also LSR no informal label alternate name derived_from derived from is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) A core relation that holds between a part and its whole. a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of part of http://www.obofoundry.org/ro/#OBO_REL:part_of https://wiki.geneontology.org/Part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) A core relation that holds between a whole and its part. a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part has part realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility 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 To say that b realizes c at t is to assert that there is some material entity d and b is a process which has participant d at t and c is a disposition or role of which d is bearer_of at tand the type instantiated by b is correlated with the type instantiated by c. 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 realises realizes precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes Inverse of occurrent_part_of which is defined as: b occurrent_part_of c =Def. b is a part of c and b and c are occurrents. has process part Inverse of process_profile_of. has process attribute This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. Is about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about is about A relation between a continuant and a process, in which the continuant is somehow involved in the process. participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. consumes has input https://wiki.geneontology.org/Has_input P has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. (occurrent/continuant) has output A mereological relationship or a topological relationship Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. https://en.wikipedia.org/wiki/Causality The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities A relation that holds between a research study and the human population that it is investigating. investigates A relationship that specifies the context in which a process happens. has context A causal relation that holds between two entities where one is an intervention or its scenario and the other is an entity that is brought into existence, caused to occur, destroyed, prevented from occurring or changed by the other. has intervention outcome Discussed External A study design that includes specification of some intervention as part of the study process. controlled trial, study with at least one comparator group experimental study design This class is for any study in which an activity is undertaken for the purposes of the study, usually for the purpose of evaluating its effect. interventional study design LSR 3 Discussed A plan specification that describes the way a research study should be conducted in terms of what kind of data are collected, how the data are collected and the circumstances in which they are collected. The design is the specification that may be realised as a research study. study design External Proposed A personal attribute in which the symptoms of a person suffering from a disorder have reverted from a desired level to an undesired level. relapsed to a disorder LSR 3 Having chicken pox, asthma, a heart attack External Published A personal attribute that is the state of an individual's mental or physical condition. health status attribute LSR 3 health condition External Published A human population who are exposed to an intervention. The definition of intervention population (A human population who are exposed to an intervention) does not imply an explicit assignment to an intervention arm. While some interventions will have study designs in which researchers explicitly assign participants to intervention and control groups, this is not the case for all interventions (e.g., policy changes or public health campaigns). intervention population LSR 3 External Published A history that is of a person. sum of multiple experienced events A person's history includes the sum of their experiences, which can include experiences relating to their cultural, social and economic context. personal history External Published A population statistic about biological sex. The aggregate of biological sex in a population. biological sex population statistic sex External Published A population statistic about female biological sex. The aggregate of female biological sex in a population. female biological sex population statistic LSR 3 female sex External Published A(n) female biological sex population statistic that is the proportion of people that have a female biological sex in the population. The proportion of female biological sex in a population. proportion female biological sex population statistic LSR 1 proportion of females External Published A population statistic about female gender. The aggregate of female gender in a population. female gender population statistic External Published A(n) female gender population statistic that is the proportion of people that have a female gender in the population. The proportion of female gender in a population. proportion female gender population statistic External Published A population statistic about gender identity. The aggregate of gender identity in a population. gender identity population statistic External Published A population statistic about human age. The aggregate of human age in a population. human age population statistic LSR 1 age External Published A(n) human age population statistic that is the mean value of human age in the population. The mean of human age in a population. mean human age population statistic mean age Examples of interventions are putting health warnings on cigarette packets, providing free stop smoking services and banning smoking in public places. External Published A planned process that has the aim of influencing an outcome. intervention Includes individual human behaviour, mental activity and physiological activity. Also includes undesirable outcomes, such as treatment side effects, and unintended negative consequences of the intervention. External Published An entity that is influenced by an intervention An entity that is influenced by an intervention. intervention outcome LSR 3 External Published A process that is produced by a person. individual human activity target population External Published An object aggregate that consists of two or more people. This entity represents any group consisting of two or more people. It could range for example from small groups, neighbourhoods, and organisations to entire national populations. human population This is intended to provide a user-friendly way of representing the way in which processes are manifest. This is somewhat similar to, but not the same as, the class 'specifically dependent continuant' in Basic Formal Ontology which provides a way of representing features of material entities such as age and size. It is formally equivalent to process profile in Basic Formal Ontology. Published A process profile that is an attribute of a process. process attribute Published An attribute of a communication process. Communication processes can have a variety of attributes, such as their speed, how they are delivered, what language they take place in and the tone of voice in which they occur. All these types of attributes and more are captured by "communication process attribute" communication process attribute External Published A particular manner of communicating aimed at inducing or avoiding certain kinds of responses in others, or demonstrating certain characteristics of the initiator. communication style External Published A communication style that is an attribute of an intervention content communication process. An intervention can include various different styles of delivery for different parts of the intervention. The definition of "intervention style of delivery" is based on two other entities, namely "communication style" and "intervention content communication process". Their definitions are presented below. communication style (BCIO:044004): A particular manner of communicating aimed at inducing or avoiding certain kinds of responses in others, or demonstrating certain characteristics of the initiator. intervention content communication process (BCIO:044001): A communication that transmits the content of an intervention Note that an intervention is a planned process with the aim of influencing some outcome whereas a behaviour change intervention is an intervention that aims to influence human behaviour as an outcome. when a communication style is used as part of an intervention content communication process, then it qualifies as an intervention style of delivery intervention style of delivery External Published A planned process by which intervention content is delivered. This class intends to represent the actual delivery of an intervention, whereas the class "mental health intervention scenario plan" refers to the planned intervention, including the planned delivery of an intervention. Distinguishing between these two classes allows for the assessment of intervention fidelity. To capture planned delivery, researchers could annotate both the class "intervention delivery" and "mental health intervention scenario plan". The definition of "intervention delivery" states that it is "a planned process by which intervention content is delivered," which refers to the actual execution of the intervention. This phrasing reflects that the intervention was designed and planned in advance before being implemented, thereby making it a "planned process". intervention delivery External Published A planned process that is part of an intervention and is intended to be causally active in influencing the intervention outcome. Based on http://humanbehaviourchange.org/ontology/BCIO_007000 intervention content LSR 2 External Published A specifically dependent continuant that inheres in a person. The BCIO population ontology individuals branch defines many personal attributes Attributes included under this header are age, immigration, social and economic conditions. Includes everything that can be said about a person: the most general class under which all other qualities, dispositions, roles etc belong. personal attribute External Published A process that is part of a personal history. A process that is part of a personal history. experienced event personal history part attendance to intervention sessions, participation in intervention activities, emotionally engaging with intervention content External Published An individual human activity of an intervention participant within one or more parts of the intervention. Engagement can involve cognitive, emotional and behavioural engagement with an intervention. participant engagement with intervention Proposed A data item about the number of people in a population. number of people in a population Percentage of highly educated individuals in a population. Mean age in a population. External Proposed A data item that is about the number or extent of something in a population. population statistic entity Entity entity Julius Caesar Verdi’s Requiem the Second World War your body mass index An entity is anything that exists or has existed or will exist. 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]) https://www.wikidata.org/wiki/Q35120 entity entities entitātem 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. 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 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) (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 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 (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] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] true 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. 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] true 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. 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]) anatomical entity (BFO) 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] true A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] 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. External 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] BFO:0000015 An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. 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 External b is a disposition means: b is a realizable entity and b’s bearer is some material entity and b is such that if it ceases to exist, then its bearer is physically changed, and b’s realization occurs when and because this bearer is in some special physical circumstances, and this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) 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 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 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] sdc SpecificallyDependentContinuant specifically dependent continuant 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 External 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]) b is a specifically dependent continuant = Def. b is a continuant and 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 (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (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] true 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. characteristic specifically dependent continuant specifically dependent continuant https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 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. per discussion with Barry Smith (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (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 External 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 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] object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. External b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate object aggregate LSR 3 An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] gdc GenericallyDependentContinuant generically dependent continuant 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]) 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] 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. 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] 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. External A one-dimensional temporal region is a temporal region that is extended. 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 one-dimensional temporal region LSR 1 LSR 3 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 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 External An <independent continuant> that is spatially extended whose identity is independent of that of other entities and can be maintained through time. 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. Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. 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] process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] history History External A process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. A process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) A quantitative or qualitative value which is the result of an act of assessing a morphological or physiological state or property in a single individual or sample or a group of individuals or samples, based on direct observation or experimental manipulation. clinical_measurement_ontology CMO:0000000 clinical measurement A quantitative or qualitative value which is the result of an act of assessing a morphological or physiological state or property in a single individual or sample or a group of individuals or samples, based on direct observation or experimental manipulation. American_Heritage:The_American_Heritage_Dictionary_of_the_English_Language--4th_Ed Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart and/or blood vessels. EFO:0004298 EFO:0006919 cardiovascular event measurement clinical_measurement_ontology CMO:0000001 cardiovascular measurement Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart and/or blood vessels. American_Heritage:The_American_Heritage_Dictionary_of_the_English_Language--4th_Ed Dorland:Dorlands_Illustrated_Medical_Dictionary--31st_Ed ISBN:978-1416049982 A quantification of a parameter of the chemical composition of blood. clinical_measurement_ontology blood molecular composition measurement CMO:0000023 blood chemistry measurement A quantification of a parameter of the chemical composition of blood. ISBN:978-0323057479 Mosby:Mosbys_Manual_of_Diagnostic_and_Laboratory_Tests--4th_Ed Any measurement involving the amount, composition or type of protein, the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, in blood. total blood protein measurement EFO:0004536 EFO:0005105 EFO:0007937 VT:0005416 clinical_measurement_ontology CMO:0000028 blood protein measurement Any measurement involving the amount, composition or type of protein, the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, in blood. Dorland:Dorlands_Illustrated_Medical_Dictionary--31st_Ed ISBN:978-1416049982 A measurement of the blood, it's contents, cells or other factors contained within the blood. EFO:0004503 hematological measurement clinical_measurement_ontology CMO:0000035 blood measurement A measurement of the blood, it's contents, cells or other factors contained within the blood. RGD:MS External Any measurement of components of the electrical conduction system of the heart.The electrical conduction system of the heart transmits signals generated usually by the sinoatrial node to cause contraction of the heart muscle. mshimoyama 2010-06-17T10:36:15Z EFO:0007885 JT interval clinical_measurement_ontology CMO:0000230 heart electrical conduction measurement External QT interval corrected for heart rate calculated by the QT interval divided by the square root of the interval from one QRS complex to the onset of the next QRS complex measured in seconds. mshimoyama 2010-06-17T12:40:52Z clinical_measurement_ontology CMO:0000269 QTC interval LSR 3 QT interval corrected for heart rate calculated by the QT interval divided by the square root of the interval from one QRS complex to the onset of the next QRS complex measured in seconds. http://en.wikipedia.org Measurement of the amount in blood of a molecular chain compound composed of two or more amino acids joined by peptide bonds that is produced in one part or organ of the body and initiates or regulates the activity of an organ or a group of cells in another part of the body. mshimoyama 2010-06-25T12:08:08Z EFO:0004504 serum hepcidin measurement clinical_measurement_ontology CMO:0000286 blood peptide hormone level Measurement of the amount in blood of a molecular chain compound composed of two or more amino acids joined by peptide bonds that is produced in one part or organ of the body and initiates or regulates the activity of an organ or a group of cells in another part of the body. Mosby:Mosbys_Medical_Dictionary--8th_Ed Any measurement of a structural part of a system of the body that is composed of tissues and cells that enable it to perform a particular function. JSmith 2012-02-15T05:00:53Z clinical_measurement_ontology CMO:0000669 organ measurement Any measurement of a structural part of a system of the body that is composed of tissues and cells that enable it to perform a particular function. Mosby:Mosbys_Medical_Dictionary--8th_Ed JSmith 2012-02-15T05:06:19Z clinical_measurement_ontology CMO:0000670 This is not the same term as the original "heart measurement". That term is now "heart morphological measurement". heart measurement Measurement of the amount in blood of any complex chemical substance produced in one part or organ of the body that initiates or regulates the activity of an organ or a group of cells in another part of the body. JSmith 2012-08-02T03:51:38Z hormone measurement EFO:0004730 clinical_measurement_ontology CMO:0001003 blood hormone level Measurement of the amount in blood of any complex chemical substance produced in one part or organ of the body that initiates or regulates the activity of an organ or a group of cells in another part of the body. Mosby:Mosbys_Medical_Dictionary--8th_Ed External The amount of prolactin found in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. Prolactin is a peptide hormone which is secreted by the anterior pituitary and is involved in lactation, growth regulation for tissues including cells of the immune system, and possibly supression of apoptosis. A peptide hormone is a complex organic compound that contains carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, and that is produced in one part or organ of the body and initiates or regulates the activity of an organ or a group of cells in another part of the body. JSmith 2013-10-14T16:49:10Z MESH:D011388 VT:0005121 clinical_measurement_ontology blood Prl level CMO:0001822 blood prolactin level LSR 3 The amount of prolactin found in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. Prolactin is a peptide hormone which is secreted by the anterior pituitary and is involved in lactation, growth regulation for tissues including cells of the immune system, and possibly supression of apoptosis. A peptide hormone is a complex organic compound that contains carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, and that is produced in one part or organ of the body and initiates or regulates the activity of an organ or a group of cells in another part of the body. Dorland:Dorlands_Illustrated_Medical_Dictionary--31st_Ed ISBN:978-1416049982 Mosby:Mosbys_Medical_Dictionary--8th_Ed RGD:736187 Saunders:Saunders_Comprehensive_Veterinary_Dictionary--3rd_Ed characteristic measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. External A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label measurement unit label LSR 1, LSR 2, LSR3 LSR3 unit datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. datum label data item Data items include counts of things, analyte concentrations, and statistical summaries. External An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item data item LSR 1 LSR 2 information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. External A generically dependent continuant that is about some thing. A generically dependent continuant that is about some thing. An information entity is an entity that represents information about some other entity. For example, a measurement, a clustered data set. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). Pier: 'data, information or knowledge'. OR 'representation' information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. James Malone PERSON: Chris Stoeckert OBI_0000142 information http://www.ebi.ac.uk/efo/EFO_0001435 true an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity information content entity information content entity information content entity information entity LSR 1 directive information entity External An information content entity whose concretizations indicate to their bearer how to realize them in a process. An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity directive information entity plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. External A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg Clint Dowland OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification plan specification https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. External A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum measurement datum LSR 1 LSR 3 textual entity Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities External A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. PERSON: Lawrence Hunter text textual entity textual entity LSR 1 External An extended organism that is a member of the species Homo sapiens. person human being person External A bodily process that occurs in the brain, and that can of itself be conscious, or can give rise to a process that can of itself be conscious or can give rise to behaviour. A 'mental process' is a subclass of 'bodily process', as mental processes occur within the body, specifically involving the brain. A bodily process which brings into being, sustains or modifies a cognitive representation or a behavior inducing state. Examples include thinking, feeling pain, remembering and emotion as occurrent experiences. Mental processes can varying in the degree to which they involve consciousness. mental process GO:0050890, cognition, defined as `The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.' LSR 3 LSR3 External A bodily disposition is a disposition that inheres in some extended organism. A bodily disposition is a disposition that inheres in some extended organism. Examples are: my disposition to catch a cold when exposed to a virus, my ability to speak the English language. personal disposition Bodily disposition includes features that can be used in a specific context, such as a person's strength, but not a person's weight. A person has a specific weight independent of the circumstances they are in. Extended organism refers to an organism and its microbiome (e.g., the bacteria that live in one's digestive system). bodily disposition bodily disposition LSR 1 External A mental disposition is a bodily disposition that is realized in a mental process. A mental disposition is a bodily disposition that is realized in a mental process. 'Mental disposition' is a subclass of 'bodily disposition', as mental dispositions occur in the body. mental disposition mental disposition LSR 3 External An information content entity that represents a type of scale on which a variable is measured, including nominal, ordinal, interval, ratio. Marcy Harris level of measurement scale of measure WEB: http://en.wikipedia.org/wiki/Level_of_measurement measurement scale LSR 3 External A quantitative confidence value that measures the variability of data around the mean. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms standard deviation LSR 2 LSR 3 A data item that is derived from a statistical data analysis. Jie Zheng, Yongqun He, Marcy Harris, Asiyah Yu Lin statistic WEB: http://en.wikipedia.org/wiki/Statistic WEB: http://www.ask.com/question/what-is-numerical-data derived data from statistical analysis A data item that is derived from an inferential statistical data analysis. Jie Zheng, Yongqun He inferential statistic WEB: http://psc.dss.ucdavis.edu/sommerb/sommerdemo/stat_inf/intro.htm WEB: http://www.ask.com/question/what-is-numerical-data derived data from inferential statistical analysis A data item that is produced as the output of a data transformation. Person: Jie Zheng, Oliver He transformed data item obsolete planned process planned process Injecting mice with a vaccine in order to test its efficacy External A process that realizes a plan which is the concretization of a plan specification. A process that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) obsolete planned process planned process planned process true quantitative confidence value External A data item which is used to indicate the degree of uncertainty about a measurement. A data item which is used to indicate the degree of uncertainty about a measurement. person:Chris Stoeckert group:OBI quantitative confidence value quantitative confidence value LSR 1 plan The plan of researcher X to perform an experiment according to a protocol. External A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a completely executed planned process. A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. AR, BP, JM, MC, PRS branch derived plan plan LSR 1 average value External A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. PERSON: James Malone PERSON: Monnie McGee arithmetic mean average value average value LSR 2 LSR 3 study design a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. External A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design study design LSR 3 External A process in which at least one bodily component of an organism participates. A process in which at least one bodily component of an organsim participates. Albert Goldfain http://www.jbiomedsem.com/content/1/1/10 creation date: 2009-06-23T11:53:49Z From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060 bodily process External A bodily process that is clinically abnormal. A bodily process that is clinically abnormal. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:54:29Z pathological bodily process LSR 3 External An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=3 creation date: 2010-01-25T04:51:11Z From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087 extended organism A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATO:0000072 quality PATO:0000001 quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG External A physical quality inhering in a bearer that has mass near a gravitational body. A physical quality inhering in a bearer that has mass near a gravitational body. Important usage note: Note that this ontology has a class for a similar concept, mass (PATO:0000125). Mass and weight are not equivalent. For most use cases, the class mass is strongly preferred over weight. quality PATO:0000128 For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism. weight LSR 3 A physical quality inhering in a bearer that has mass near a gravitational body. Important usage note: Note that this ontology has a class for a similar concept, mass (PATO:0000125). Mass and weight are not equivalent. For most use cases, the class mass is strongly preferred over weight. Wikipedia:http://en.wikipedia.org/wiki/Weight https://en.wikipedia.org/wiki/Mass#Weight_vs._mass A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0002079 Wikipedia:Physical_property relational physical quality quality PATO:0001018 physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATOC:GVG External A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum. force amplitude quality PATO:0001035 force LSR 3 A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum. thesaurus.maths:thesaurus.maths A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality A quality which inheres in a continuant. PATOC:GVG A planned process executed in the performance of scientific research wherein systematic investigations are performed to establish facts and reach new conclusions about phenomena in the world. Data generation process are typically experimental studies or observations, but can include any process generating information used to evaluate a claim. This is an organizational class that groups more specific types of such processes that are most commonly used in generating data used as evidence to support claims. These processes produce informational artifacts such as measured data values, derived statistical calculations and confidence measures, or statements representing summaries or conclusions drawn from such data. research activity External A planned process that executes some study design or protocol to generate scientific data that is interpreted to test or generate a hypothesis. Explore the classification of study types here as a possibility to implement in SEPIO. https://mcw.libguides.com/evidencebased/studies Useful because these map to the strength of the evidence each might provide. A research study is considered broadly to be any scientific activity aimed at answering a research question. Studies can be simple or complex, depending on the scope of the question being explored and the extent of resources deployed in doing so. They may include a full research investigation, a set of experiments, or a single experiment or assay. Regardless, that act of summarizing any results as a finding statement is considered part of the study. A research study is considered broadly to be any scientific activity aimed at answering a research question. Studies can be simple or complex, depending on the scope of the question being explored and the extent of resources deployed in doing so. They may include a full research investigation, a set of related experiments, or a single experiment or assay. Regardless, that act of summarizing any results as a finding statement is considered part of the study. 'Study' here is broadly considered to include any defined activity performed to address a scientific question or generate a scientific hypothesis. It covers scientific inquiry at different scales of complexity, from a single assay, experiment or observation, to a complex research investigation addressing a broader scientific question. Studies can be based on a broad range of methods, including in silico algorithms, in vitro or in vivo experimentation on model systems, clinical studies on human subjects, or curation and analysis of existing knowledge, e.g. from publications, datasets, or knowledegbases, to derive novel insight. research study research study measure of variation or statistical dispersion is a data item which describes how much a theoritical distribution or dataset is spread. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra STATO measure of variation measure of variation measure of dispersion External a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data. a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic). statistic statistic statistic LSR 1 External A data item which denotes the smallest value found in a dataset or resulting from a calculation. a minimum value is a data item which denotes the smallest value found in a dataset or resulting from a calculation. Alejandra Gonzalez-Beltran COKA group Orlaith Burke Philippe Rocca-Serra minimum value STATO minimum observed value LSR 3 External A data item which denotes the largest value found in a dataset or resulting from a calculation. maximum value is a data item which denotes the largest value found in a dataset or resulting from a calculation. Alejandra Gonzalez-Beltran COKA group Orlaith Burke Philippe Rocca-Serra maximum value STATO maximum observed value LSR 3 External a estimate is a data item which is computed from a dataset to provide an approximated value (an estimator) for a 'statistical parameter' (a 'characteristics/parameter' of the true underlying distribution) of a real population. a estimate is a data item which is computed from a dataset to provide an approximated value (an estimator) for a 'statistical parameter' (a 'characteristics/parameter' of the true underlying distribution) of a real population. Hanna Cwiek Tom Nichols Philippe Rocca-Serra Tom Nichols STATO https://github.com/ISA-tools/stato/issues/74 estimate LSR 3 http://davidmlane.com/hyperstat/A121160.html External The standard error is a measure of dispersion applied to estimates across hypothetical repeated random samples. The standard error is a measure of dispersion applied to estimates across hypothetical repeated random samples. It is a measure of how precise an estimate of a statistical parameter is. The standard error is the estimated standard deviation of an estimate. It measures the uncertainty associated with the estimate. Compared with the standard deviations of the underlying distribution, which are usually unknown, standard errors can be calculated from observed data. Harold Lehmann, Kenneth Wilkins, Brian S. Alper, Xing Song, Joanne Dehnbostel, Muhammad Afzal, Philippe Rocca-Serra adapted from wikipedia and from SAGE research method article http://methods.sagepub.com/reference/encyc-of-research-design/n435.xml standard error of the estimate standard error of estimate https://fevir.net/resources/CodeSystem/27270#STATO:0000562 LSR 3 External a point estimate is a data item which provides a particular value evaluating a population parameter a point estimate is a data item which provides a particular value evaluating a population parameter. Hanna Cwiek Philippe Rocca-Serra Tom Nichols https://github.com/ISA-tools/stato/issues/74 point estimate point estimate LSR 3 A measurement is an information entity that is a recording of the output of a measurement such as produced by an instrument. James Malone Jie Zheng Tomasz Adamusiak true MO:144 NCIt:C25209 NIFSTD:sao279801585 SNOMEDCT:122869004 measurement The determination of the amount of hormone present in a sample. true NCIt:C74742 SNOMEDCT:122445005 hormone measurement quantification of prolactin in a sample Dani Welter http://purl.obolibrary.org/obo/OBA_1000952 3.77.0 Project to replace EFO measurement branch with enriched OBA branch. Please use: OBA:1000952 obsolete_prolactin measurement true Obsolete Class Published Dose of pharmacological substance delivered to an individual. Parent class from Ontology for Biomedical Investigations dose of pharmacological substance LSR 3 Published A process attribute whose bearer is an intervention. BCIO:050315 intervention attribute Published A material entity that is not dependent on a process but may influence the effect of the process on its outcome. material context of process Published A temporal interval between the start and end of an intervention. inspired by BCIO:008560 intervention duration LSR 3 Published An occurrent that is not dependent on a process but may influence the effect of the process on its outcome. This entity includes time periods, events, etc. temporal context of process Published An adverse event associated with a change in a person's bodily measurement parameters. Based on http://purl.obolibrary.org/obo/OAE_0000581 adverse change in a bodily measurement parameter LSR 3 Published An adverse change in a bodily measurement parameter relating to body weight. adverse change in body weight LSR 3 Published An adverse change in a bodily measurement parameter relating to prolactin measurement. adverse change in prolactin measurement LSR 3 Published A pathological bodily process that occurs after the intervention delivery starts. Based on http://purl.obolibrary.org/obo/OAE_0000001 adverse event following an intervention LSR 3 adverse event Published A drug-induced movement disorder following intervention that involves feeling restlessness, increased urges to move and reduced capability to suppress such urges. Based on https://www.ncbi.nlm.nih.gov/books/NBK519543/ akathisia following pharmacological intervention LSR 3 akathisia Published A serious adverse event following an intervention that has an outcome of death. Based on http://purl.obolibrary.org/obo/OAE_0000632 death following an intervention LSR 3 death Published Symptom severity that is associated with a depression symptom. depression symptom severity LSR 3 Published An adverse event following a pharmacological intervention that involves reduced abilities to control movements. extrapyramidal symptom following intervention "Based on https://www.ncbi.nlm.nih.gov/books/NBK534115/ Based on http://purl.obolibrary.org/obo/OAE_0000581" drug-induced movement disorder following intervention LSR 3 Published A bodily disposition to realise processes that influence a person's life quality. human functioning LSR 3 Published Psychotic disorder symptom severity that is associated with negative psychotic disorder symptoms. negative psychotic disorder symptom severity LSR 3 Published Number of participant drop-out from the study as a result the participants experiencing some adverse event. number of participant drop-out due to adverse events LSR 3 Published Number of study participants who withdraw from or cannot complete a study. number of participant drop-out from study LSR 3 Published An intervention outcome that is positively influenced by the intervention. positive intervention outcome LSR 3 Published Psychotic disorder symptom severity that is associated with positive psychotic disorder symptoms. Based on https://www.psychiatry.org/patients-families/schizophrenia/what-is-schizophrenia A measure for 'positive psychotic disorder symptom severity' positive psychotic disorder symptom severity LSR 3 Published Symptom severity that is associated with a psychotic disorder symptom. psychotic disorder symptom severity LSR 3 Published An adverse event following an intervention that results in death, a life-threatening event, a persistent or significant disability or a birth defect or requires hospitalisation or extends hospitalisation. Based on https://www.fda.gov/safety/reporting-serious-problems-fda/what-serious-adverse-event serious adverse event following an intervention LSR 3 serious adverse event Published A data item that is about the severity dimension associated with a symptom. A measure for 'psychotic disorder symptom severity' symptom severity LSR 3 Published A textual entity documenting the year in which some study was published. publication year textual entity LSR 3 publication year Published A study arm designation as a comparator to some intervention arm. control arm LSR 1, LSR 2 LSR 2 Published An information content entity that is about an intervention scenario and designates it as part of an intervention evaluation study. study arm LSR 1 LSR 1, LSR 2, LSR 3 Published A control arm designation where the same content and delivery is already provided as standard practice. treatment as usual control arm LSR 2 Published Symptom severity that is associated with anhedonia. anhedonia symptom severity LSR 1 Published A bodily disposition to detect, pursue, learn from, and derive pleasure from stimuli perceived as positive. Goodnight, J. (Ed.) (2018). . (Vols. 1-5). SAGE Publications, Inc., https://doi.org/10.4135/9781506307633 reward sensitivity LSR 1 Published Time point at which a measurement is taken with reference to a temporal part of the intervention evaluation study. temporal reference associated with measurement in intervention LSR 3 Published Symptom severity that is associated with an anxiety symptom. anxiety symptom severity LSR 1 LSR 2 Published A number of people in a population that is about the number of participants in an study or part of a study at a timepoint. number of study participants LSR 3 Published Number of study participants who were allocated to study arms within a study. number of study participants in a study arm LSR 3 Published An aggregate of entities that form the environment in which an intervention is provided. BCIO:005000 Based on http://humanbehaviourchange.org/ontology/BCIO_014000 intervention setting LSR 3 Published Symptom severity relating to a post-traumatic stress symptom. PTSD severity post-traumatic stress symptom severity LSR 2 Published An adverse event following an intervention that occurs in the digestive system. cross reference: http://purl.obolibrary.org/obo/OAE_0000439 digestive system adverse event following intervention LSR 1 digestive system adverse event Published An adverse event following an intervention that involves experiencing dizziness. cross reference: http://purl.obolibrary.org/obo/OAE_0000388 dizziness following intervention LSR 1, LSR 3 dizziness Published A digestive system adverse event following intervention that involves experiencing dry mouth. cross reference: http://purl.obolibrary.org/obo/OAE_0000505 dry mouth following intervention LSR 1 dry mouth Published A pain following intervention that has an outcome of headache. cross-reference: http://purl.obolibrary.org/obo/OAE_0000377 headache following intervention LSR 1, LSR 3 headache Published An adverse event following an intervention in which there is an inability to fall asleep or to stay asleep as long as desired. cross-reference: http://purl.obolibrary.org/obo/OAE_0002206 insomnia following intervention LSR 1, LSR 3 insomnia Published A digestive system adverse event following intervention that has an outcome of nausea, a gastric discomfort associated with the inclination to vomit cross reference: http://purl.obolibrary.org/obo/OAE_0000600 nausea following intervention LSR 1 nausea Published An adverse event following an intervention that has an outcome of pain. cross-reference: http://purl.obolibrary.org/obo/OAE_0000374 pain following intervention LSR 1, LSR 3 pain Published A digestive system adverse event following intervention that has an outcome of vomiting, the retrograde expulsion of gastric contents through the oral cavity. cross reference: http://purl.obolibrary.org/obo/OAE_0000601 vomiting following intervention LSR 1 vomiting Published A process that is causally active in the relationship between an intervention scenario and its intervention outcome. For a construct to be a mechanism of action, it must be causally active in bringing about the intervention’s effect on its outcome. However, interventions are typically designed based on hypothesised mechanisms of action, which may or may not hold true depending on factors such as population and setting. The ontology provides a structured framework for organising mechanisms of action but does not replace the need for empirical validation. The ontology does not specify the level of evidence required to confirm that a hypothesised mechanism has been realised. In other words, the ontology itself does not make causal inferences about specific mechanisms. When using the ontology, researchers can code hypothesised mechanisms within the subclasses of “intervention mechanism of action”. The assessment of whether sufficient evidence supports a causal relationship occurs at the annotation level, where empirical data validate the connections between constructs. The relationship between intervention techniques, mechanisms, and outcomes is often complex and non-linear. Multiple mechanisms of action may interact in various ways, including combinations, sequences, or feedback loops. intervention mechanism of action Published A measurement scale that is used to measure anhedonia symptom severity. anhedonia scale LSR 1 Published A measurement scale that is used to measure anxiety symptom severity. anxiety scale LSR 1 Published An information content entity about the followup data available for a study. information on available followup data LSR 1, LSR 3 Published Measurement datum that was recorded as post-intervention data in a study. measurement datum at post-intervention LSR 1, LSR 2, LSR 3 post-intervention Published A measurement scale used to measure post-intervention data in a study. measurement scale at post-intervention Published Number of study participants for whom a measurement was made. number of participants with measurement LSR 1 LSR 3 Published A measurement scale that is used to measure reward sensitivity. reward sensitivity scale LSR 1 Published An information content entity about the orientation of a measurement's scoring system in which higher numerical levels can indicate higher or lower levels of a construct. scale directionality LSR 1 Published Measurement datum that was recorded as baseline data in a study. measurement datum at baseline LSR 1 baseline Published A temporal interval between the time of data collection for pre-intervention data and post-intervention data in a study. duration between baseline and post-intervention measurement LSR 1 Published A textual entity intended to identify a particular study. study identification LSR 3 Published A number of people in a population that is about the number of people that have female biological sex. number of female biological sex LSR 3 number of females Published Number of study participants for whom an outcome has been identified within a study. number of participants with specific outcome LSR 1, LSR 3 Published An intervention evaluation study risk of bias or error associated with the allocation sequence generated and applied in a study. allocation risk of bias LSR 3 Published An information content entity that is about the likelihood of the intervention evaluation finding misrepresenting the intervention outcome. intervention evaluation study risk of bias or error LSR 3 Published An intervention evaluation study risk of bias or error associated with the delivery of the intervention. risk of bias associated with intervention LSR 3 Published An intervention evaluation study risk of bias or error associated with how outcome data was measured in a study. risk of bias associated with measurement of outcome data LSR 3 Published An intervention evaluation study risk of bias or error associated with missing outcome data in a study. risk of bias associated with missing outcome data LSR 3 Published An intervention evaluation study risk of bias or error associated with selective reporting of outcomes in the study report. risk of bias associated with selective outcome reporting LSR 3 Published An adverse event following an intervention that involves symptoms associated with anticholinergic drugs. anticholinergic symptom following intervention LSR 3 anticholinergic symptom Published A measurement scale that is used to measure depression symptom severity. depression symptom severity scale LSR 3 Published A measurement scale that is used to measure human functioning. human functioning scale LSR 3 Published A psychotic disorder symptom severity scale that is associated with negative psychotic disorder symptoms. negative psychotic disorder symptom severity scale LSR 3 Published A psychotic disorder symptom severity scale that that is associated with positive psychotic disorder symptoms. Based on https://www.psychiatry.org/patients-families/schizophrenia/what-is-schizophrenia positive psychotic disorder symptom severity scale LSR 3 Published A measurement scale that is used to measure psychotic disorder symptom severity. psychotic disorder symptom severity scale LSR 3 Published An adverse event following intervention that involves experiencing tiredness. tiredness following intervention LSR 3 tiredness Published An adverse event following an intervention that involves experiencing a prolonged QTc. QTc prolongation following intervention LSR 3 QTc prolongation Published An adverse change in a body weight relating to weight gain. adverse increase in body weight LSR 3 Published An adverse event following an intervention that involves experiencing agitation. agitation following intervention LSR 3 agitation Published An adverse event following an intervention that involves experiencing hyperprolactinemia. hyperprolactinemia following intervention LSR 3 hyperprolactinemia Published An adverse event following an intervention that involves experiencing low blood pressure. hypotension following intervention LSR 3 hypotension Published A point estimate about the mean difference between an intervention and comparison condition in a study. midpoint estimate for the mean difference of an outcome between the intervention and comparison condition LSR 3 Published A data item about the number of sequential treatments delivered to participants in a study. number of sequential treatments LSR 3 Published An adverse event following an intervention that involves feeling anxiety. anxiousness following intervention LSR 3 anxiousness Published Mental health intervention content that uses communication or recommended tasks to assess and improve a person’s adaptive mental or behavioural functioning. https://bciosearch.org/BCIO_050364 psychological intervention LSR 2 Published A control arm designation where the same dose of interpersonal interaction is provided as in the intervention group, but without any additional content from the intervention. Attention control Based on https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858509/ attention management control arm Published An intervention content that is part of a mental health intervention. mental health intervention content drug dose and number of intervention techniques (e.g., action plans, social support) Published An intervention attribute that is its amount. "Intervention dose can capture the intensity of any intervention, including social, psychological and pharmacological interventions. Intervention dose refers to the intensity or amount of an intervention, which is about the content of an intervention. In contrast, an intervention's schedule of delivery is about the temporal aspects of the intervention. There is some overlap between the entities ""intervention dose"" and ""intervention schedule of delivery"". For example, a more frequent intervention schedule with specific doses would suggest a higher overall dose of the intervention. However, ""intervention dose"" can capture concepts that are not directly relevant to the temporal organisation of the intervention, such as overall number of intervention strategies and drug dose." Intervention dose can capture the intensity of any intervention, including social, physical, psychological and pharmacological interventions. Intervention dose refers to the intensity or amount of an intervention, which is about the content of an intervention. In contrast, an intervention's schedule of delivery is about the temporal aspects of the intervention. There is some overlap between the classes "intervention dose" and "intervention schedule of delivery". For example, a more frequent intervention schedule with specific doses would suggest a higher overall dose of the intervention. However, "intervention dose" can capture concepts that are not directly relevant to the temporal organisation of the intervention, such as overall number of intervention strategies and drug dose. This class intends to represent the actual dose delivered as part of an intervention, whereas the class "mental health intervention scenario plan" refers to the planned intervention, including the planned dose of an intervention. Distinguishing between these two classes allows for the assessment of intervention fidelity. To capture planned dose, researchers could annotate both the class "intervention dose" and "mental health intervention scenario plan". intervention dose Published An intervention attribute that is the physical or informational medium through which an intervention is provided. intervention mode of delivery Published An intervention attribute that involves its temporal organisation. Temporal organisation includes different temporal dimensions, such as timing, frequency, duration and the sequence of activities. Intervention dose refers to the intensity or amount of an intervention, which is about the content of an intervention. In contrast, an intervention's schedule of delivery is about the temporal aspects of the intervention. There is some overlap between the entities "intervention dose" and "intervention schedule of delivery". For example, a more frequent intervention schedule with specific doses would suggest a higher overall dose of the intervention. However, "intervention dose" can capture concepts that are not directly relevant to the temporal organisation of the intervention, such as overall number of intervention strategies and drug dose. intervention schedule of delivery Published A role played by a person, population or organisation that provides an intervention. intervention provider The class “intervention source” has been defined to include a person, population or organisation, as these sources can be legally accountable for an intervention. A computer program or machine cannot be held accountable in the same way. Therefore, the organisation or people that provide the computer program or machine would be considered the intervention source, where relevant. When an intervention is delivered via a computer program (e.g., an app), this can be captured in the ontology through the relevant subclasses of "intervention mode of delivery". intervention source Published A planned process that is the smallest part of an intervention that is observable, replicable and on its own has the potential to influence an intervention outcome. intervention technique Published An intervention that has the aim of influencing some aspect of mental health. The "mental health intervention scenario" class captures a "mental health intervention" within a specific context, level of engagement and outcomes. Mental health interventions (represented as "mental health intervention") could be delivered in different contexts and/or have different outcomes at different times. For example, we could deliver the same intervention ("mental health intervention") two years after its previous delivery or in a different context ("mental health intervention scenario"), and this could lead to different outcomes. mental health intervention Published A planned process in which a mental health intervention is applied in a given context. The "mental health intervention scenario" class captures a "mental health intervention" within a specific context. Mental health interventions (represented as "mental health intervention") could be delivered in different contexts and/or have different outcomes at different times. For example, we could deliver the same intervention ("mental health intervention") two years after its previous delivery or in a different context ("mental health intervention scenario"), and this could lead to different outcomes. mental health intervention scenario planned Published A history that is of a population. experiences can be captured as 'personal history part'. is an aggregate of personal history population history Published A process context in which the process is an experience. BCIO:005000 context of experience Published A process context in which the process is an intervention. BCIO:005000 intervention context Published A temporal context of a process where the process is the intervention. BCIO:047000 intervention temporal context Published A data item that is about a collection of aggregate symptom severity. aggregate symptom severity LSR 3 severity of condition Published A directive information entity that indicates how outcomes of an intervention were obtained. datatype for outcome LSR 3 Published A digestive system adverse event following an intervention that involves the abnormally delayed or infrequent passage of dry hardened feces. http://purl.obolibrary.org/obo/SYMP_0019180 constipation adverse event following intervention LSR 1 constipation Published Number of study participants for whom a drop-out assessment was made. number of participants with drop-out assessment LSR 3 Published A measurement scale that is used to measure mental processes. mental process scale LSR 3 Published A plan that is realized in a mental health intervention scenario process. BCIO:028000 This class is intended to represent the planned content or delivery of an intervention, whereas the class "mental health intervention scenario" refers to the intervention as it was actually implemented. Distinguishing between these two classes allows for the assessment of intervention fidelity. mental health intervention scenario plan LSR 1 Published A textual entity that refers to the digital object identifier of a research study. digital object identifier Published Mental health intervention content that uses pharmacological substances to assess and improve a person’s adaptive mental or behavioural functioning. pharmacological intervention LSR 1, LSR3 Published A measurement scale that is used to measure post-traumatic stress symptom severity. post-traumatic stress symptom severity scale LSR 2 Published Mental health intervention content that uses physical performance behaviour to assess and improve a person’s adaptive mental or behavioural functioning. GMHO:0000239 BCIO:036042 physical activity intervention LSR 2 Published Dose of physical activity intervention delivered to an individual. dose of physical activity intervention 2 Published A health status attribute that is the state of an individual´s mental condition. mental health status attribute LSR 3 mental health condition Published A number of people in a population that is about the number of people that have female gender. number of female gender Proposed An entity that includes the material and temporal contexts that are not part of but may influence the outcome of a process. process context Proposed A measurement scale that is used to measure a belief about quality of life. belief about quality of life scale LSR 6 Proposed A measurement scale that is used to measure a cognitive bias. cognitive bias scale LSR 6 Proposed An anxiety scale that is used to measure social anxiety symptom severity. social anxiety scale LSR 6 Proposed Anxiety symptom severity that is associated with social anxiety. social anxiety symptom severity LSR 6 Proposed An intervention content that uses tasks to assess and modify a person’s cognitive bias dispositions. cognitive bias modification intervention LSR 6 Proposed A data item that is the number of contact events in a mental health intervention temporal part. number of mental health intervention contact events LSR 6