Ontology for Scientific Evidence and Provenance Information The SEPIO ontology is in its early stages of development, undergoing iterative refinement as new requirements emerge and alignment with existing standards is explored. 2023-06-13 editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term example of usage 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> example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition 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.obofoundry.org/obo/obi> editor note term editor 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 https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative label 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. 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 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 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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 curator note 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 term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive consider 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 usage note in_value_set sepio_preferred_label Annotation indicating whether a property represents a "shortcut" relation that can be used to directly link two objects that are indirectly linked through a longer path of two or more edges. Shortcut relations can be logically expanded to be expressed in terms of this longer path, e.g. has_evidence_from_source = has_evidence_line o has_evidence_item o source. is_shortcut eco subset An account of the resource. Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource." description database_cross_reference database_cross_reference in_subset is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of part of http://www.obofoundry.org/ro/#OBO_REL:part_of realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes executed by has specified input is specified input of has specified output is specified output of inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of has characteristic has characteristic https://github.com/oborel/obo-relations/pull/284 participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in is concretized as this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps true w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y This is the transitive form of the develops from relation develops from inverse of develops from develops into p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. negatively regulates (process to process) negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. positively regulates (process to process) positively regulates c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. has function in capable of part of true Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y has developmental contribution from inverse of has developmental contribution from developmentally contributes to Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within Inverse of developmentally preceded by developmentally succeeded by p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. causally upstream of, negative effect q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of inheres in part of characteristic of part of true A mereological relationship or a topological relationship Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. false part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p actively involved in enables part of involved in inverse of enables enabled by inverse of regulates regulated by (processual) regulated by inverse of negatively regulates negatively regulated by inverse of positively regulates positively regulated by An organism that is a member of a population of organisms Is member of is a mereological relation between a item and a collection. is member of is a mereological relation between a item and a collection. is member of member part of SIO member of member of Has member is a mereological relation between a collection and an item. has member is a mereological relation between a collection and an item. SIO has member has member inverse of has input Chris Mungall input of x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y has potential to developmentally contribute to x has the potential to develop into y iff x develops into y or if x is capable of developing into y has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y has potential to directly develop into inverse of upstream of causally downstream of immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. indirectly activates indirectly positively regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly inhibits indirectly negatively regulates relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. https://en.wikipedia.org/wiki/Causality p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. causally upstream of p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. immediately causally upstream of p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 influences (processual) affects causally upstream of or within inverse of causally upstream of or within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union involved in or reguates involved in or involved in regulation of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. molecularly controls directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. directly inhibits molecularly decreases activity of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. directly activates molecularly increases activity of directly positively regulates activity of This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) is kinase activity A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities causally influenced by (entity-centric) causally influenced by interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ molecular interaction relation helper property The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). causally influences (entity-centric) causally influences p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. A relationship between a piece of evidence and an entity that plays a role in supporting that evidence. is_evidence_supported_by In the Gene Ontology association model, this corresponds to the With/From field is evidence with support from is_evidence_with_support_from Do not use this relation directly. It is a grouping relation. related via evidence or inference to p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) directly positively regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) directly negatively regulates A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. 2017-12-26T19:45:49Z realized in response to stimulus Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. 2018-01-25T23:20:13Z enables subfunction 2018-01-26T23:49:30Z acts upstream of or within, positive effect 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative 2018-01-26T23:53:22Z acts upstream of, negative effect 2018-03-13T23:55:05Z causally upstream of or within, negative effect 2018-03-13T23:55:19Z causally upstream of or within, positive effect A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. triggered by process realized in response to https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit triggered by process RO:cjm The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. regulates activity of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. pg 2022-09-26T06:07:17Z indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. pg 2022-09-26T06:08:01Z indirectly regulates A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. negatively regulates characteristic A relation between a proposition and information that supports its validity, based on the evaluation of some agent. Mapping to related terms: Consider: http://semanticscience.org/resource/SIO_000206 ! 'is supported by' has_supporting_evidence_line A relation between a proposition and information that contradicts its validity, based on the evaluation and conclusion of some agent. Mapping to related terms: Consider: http://semanticscience.org/resource/SIO_000774 ! 'is refuted by' has_conflicting_evidence has_refuting_evidence_line has_disputing_evidence_line A relation between a proposition and information that was used to evaluate a particular proposition, but failed to provide conclusive support for or against its validity. Mapping to related terms: Consider: http://semanticscience.org/resource/SIO_000207 ! 'is disputed by' has_insignificant_evidence_line A relation between a proposition and information that does not conclusively support or contradict its validity, based on evaluation of some agent. has_inconclusive_evidence_line A relation holding between a proposition and an assertion in which it is expressed. is_asserted_in A particular proposition can be asserted in more than one assertion - in cases where assertions made by different agents, or on different occasions, put forth the same proposition as true. proposition_asserted_in Decided that a more generic has_subject property should suffice to cover links from either an assertion or a proposition to an entity representing the subject of the statement made. But wanted to maintain the text in the comment here for future reference/use. Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents. As a proposition-level entity, a particular association can be expressed in more than one assertion made by different agents, or at different times. The meaning of an assertion can be captured through its link to an association whose meaning is formally specified as described above (e.g. :assertion1 is_asserted_in :association1, :association1 has_subject :thing1). The assertion_has_subject property allows more direct specification of assertion meaning, bypassing an association and pointing directly to the subject of the reified triple. In this sense, it is a shortcut relation over two more fundamental properties (is_asserted_in o association_has_subject). This property is useful when a particular dataset wants to describe statements at the level of assertions rather than propositions, and formally describe assertion semantics without needed to represent an proposition-level association. assertion_has_subject Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents. As a proposition-level entity, a particular association can be expressed in more than one assertion made by different agents, or at different times. The meaning of an assertion can be captured through its link to an association whose meaning is formally specified as described above (e.g. :assertion1 is_asserted_in :association1, :association1 has_object :thing1). The assertion_has_object property allows more direct specification of assertion meaning, bypassing an association and pointing directly to the object of the reified triple. In this sense, it is a shortcut relation over two more fundamental properties (is_asserted_in o association_has_object). This property is useful when a particular dataset wants to describe statements at the level of assertions rather than propositions, and formally describe assertion semantics without needed to represent an proposition-level association. assertion_has_object Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents. As a proposition-level entity, a particular association can be expressed in more than one assertion made by different agents, or at different times. The meaning of an assertion can be captured through its link to an association whose meaning is formally specified as described above (e.g. :assertion1 is_asserted_in :association1, :association1 has_predicate :thing1). The assertion_has_predicate property allows more direct specification of assertion meaning, bypassing an association and pointing directly to the predicate of the reified triple. In this sense, it is a shortcut relation over two more fundamental properties (is_asserted_in o association_has_predicate). This property is useful when a particular dataset wants to describe statements at the level of assertions rather than propositions, and formally describe assertion semantics without needed to represent an proposition-level association. assertion_has_predicate A relation holding between a planned process, or the artifact it generates, and a plan specification that specifies all or part of the process (e.g. a protocol, guideline, rule set) Consider SIO:00339 (a relation between a product and the information content entity that specifies it.) In SEPIO, this property is most often used to link an assertion (the generated artifact) to an 'assertion method' that may specified how it was created. This assertion method may describe what types of data may be used as evidence, what weight to give a particular type of evidence, and how to combine different lines of evidence in generating the final assertion. was_specified_by If we start using the 'study data set' class in a similar way to organize data items from a partiular study, we should create a similar property chain that traverses the property we use to link study data sets to their data item parts. Can this just be "has part" . . .or is a specific/unique relation needed here to avoid unwanted entailments? This property chain ensures that any evidence items that are organized into groups using a 'study finding' object will still be classified as evidence items for the relevant evidence line, and returned by queries for evidence items for a particular evidence line. A relation that links an evidence line to any activities (studies, assays, computational tasks, curation) that generated evidence items contributing to it. has_evidence_item_output_from has_supporting_activity true evidence_has_supporting_activity has_equivalent_proposition is_equilavent_to has_consistent_proposition is_consistent_with Previosly implemented property chains: is_asserted_in o strongly_contradicts o asserts -> strongly_contradicts asserts o strongly_contradicts o is_asserted_in -> strongly_contradicts But these broke reasoner - "the given hierarchy is not regular" error message". Apparently breaks rule that "in property chains of 3 or larger, the inner property must not also appear as the composite property". (https://arxiv.org/pdf/1212.2902.pdf) has_contradicting_proposition Relation between two propositions that make opposing claims (e.g. proposition1 holds that variant1 is pathogenic for disease1, and proposition2 holds that variant1 is benign for disease1). strongly_contradicts has_inconsistent_proposition contradicts Relationship between a statement or proposition and a document in which it is expressed (e.g. a publication, report, or database record). is_reported_in is_expressed_in Relationship between a document (e.g. a publication, report, database record) and an assertion or proposition that is stated in its content. expresses Grouping class to hold exploratory relationships linking assertions or propositions based on the compatability or degree of agreement in their meaning. Has utility toward inferring links between evidence lines and propositions. has_concordance propositional relationships has_compatability A relation between a planned process and a parameter that it measures as part of an assay or observation. measures_parameter conflicts_with aligns_with A relation that holds between an evidence line and a citable document from which information supporting the evidence line was obtained (i.e. a "supporting reference"). Note that this relation only links an evidence line to publications actually consulted by the asserting agent to find and interpret evidence items. There may be other publications that describe the same evidence item that the asserting agent did not consult, which would not qualify as supporting references. For example, consider a GO curator's use of sequence data for the rat Vegfa gene in a line of evidence supporting their assertion that the human VEGFA ortholog exhibited the same angiogeneic activity. There may be multiple publications that report this same rat gene sequence, but only the publication that the curator consulted in making this assertion would qualify as a supporting reference for this evidence line. For this resaon, we are not able to create a property chain declaring "has_evidence_item o is_described_by -> has_evidence_item_described_by". . . because this would entail that any publication describing this rat Vegfa gene sequence was a supporting reference for the assertion. has_support_from_source has_supporting_reference Keeping the label has_supporting_reference instead of has_evidence_item_described_by because the later follows the pattern we use for true shortcut relations (i.e. that can be defined using property chains). For reasons outlined in the editor note, this is not such a shortcut relation. evidence_has_supporting_reference is_inconsistent_with A relation holding between a generated artifact and an agent who evaluated its quality, completeness, or utility. In SEPIO, the agent responsible for a particular evidence line is linked via the "evaluated_by" property. This reflects that perspective that evaluation of the relevance, strength, and direction of an evidence line w.r.t. a particular assertion are the key acts inherent in the evidence line's "creation". We avoid using a "creator" relation here because this label is used in established standards such as PAV and DC to specifically describe agents contributing to a specific digital representation, as opposed to agents responsible for generating the underlying information content these concrete representations express. A explicit commitment to this more abstracted level of representation is a core feature of the SEPIO model, and has implications for how instances in the data are described, identified, and distinguished in practice. assessed_by evaluated_by A relation used to indicate context in which a particular assertion or proposition applies. has_qualifier A relation used to link an assertion or proposition to a source where evidence for it was found (i.e. a document, document part, database, etc) cito:cites_as_evidence Note that this may not qualify as a proper shortcut (i.e. it may not be valid to define using a property chain) for the same reason has_supporting reference is not defined as a property chain called has_evidence_item_described_by. true This is a shortcut relation to be used when publications are referenced as providing support for an assertion, but it is not clear how many evidence lines are described across these publications. In such cases, discrete evidence lines cannot be created, and the has_evidence_from_source relation is used to directly link the assertion to publications providing some form of evidence information. has_evidence_from_source A relation used to link an assertion or proposition directly to some indicator of the strength of the total evidence that asserting agent beleives to support it. has_total_evidence_strength This relation links an assertion or proposition directly to some indicator of the strength of the total evidence supporting it. It is used when there is not enough information to create evidence line(s) for the assertion, but the source provides some indication of the strength of the evidence supporting it. Note that this is different than the notion of statement confidence, which describes how confident an agent is that a statement is true. Confidence may depend on factors in addition to the strength of the evidence (e.g. who made the prior probability that the asserted proposition could be true, who made the assertion and when, etc.) has_evidence_level A relation between an information content entity and an agent who made a contribution to its information content, or to its subsequent modification or assessment. SEPIO intentionally creates its own hierarchy of contributor properties, instead of re-using terms from existing standards like PAV or Dublin Core - whose domain is structured digital resources. This is because properties such as pav:createdBy specifically describe agents who generated a specific digital representation of information, while SEPIO aims to describe agents responsible for generating the abstract information content that such a concrete representation may express. The subject of 'contributor' relations in the SEPIO are explicitly abstract in nature - considered at the level of their information content as opposed to concretizations in particular digital resources or representations. For example, the SEPIO "stated_by" relation explicitly refers toan agent originally putting forth a statement as true (generating its information content), as opposed to an agent creating a specific digital representation of the statement (generating a particular concretized artifact such as a json object returned by an API). Should further clarification become available with respect to whether PAV or DC contributor properties accommodate the nuanced definitions we require, we will re-consider their inclusion in SEPIO. For example, the pav:authoredBy property seems to refer specifically to the agent who generated information content expressed in a resource - and thus may be appropriate in the context of SEPIO. But even here, the range of the property is a particular authored digital resource, and not the information content it expresses. DC properties such as dc:contributor and dc:creator are ambiguous as to which level of contribution they describe. has_contributor A relation holding between a statement and an agent that validates its truth or accuracy - typically by reviewing the provenance and data on which it is based. validity_assessed_by validated_by evidence_strength_assessed_by ClinGen not using this, as they create contrigution objects and assign roles to capture such information. Can bring it back if there is need in some other use case/application. obsolete_evidence_assessed_by true A relation holding between an artifact and a contribution made by a particular agent to its creation, modification, assessment, or destruction. Consider sup-properties specific to the type of contribuion make, to support property chains for inferring a direct realtiomnship between the artifact/entitiy contributed to, and a related agent or date. At present, we could only support: - qualified_contribution o date_of_contribution -> dc:date Want to be able to support inferences such as: - qualified_creation o date_of_contribution -> date_created - qualified_evaluation o date_of_contribution -> date_evaluated - qualified_modification o date_of_contribution -> date_modified has_contribution Analogous to PROV qualified Attribution - use to capture additional information about the contribution made by an agent, such as a role they played, or organization on behalf of which the contribution was made. qualified_contribution A relation between an information entity and an indicator of degree of confidence that the information it represents is true. trust_rating Confidence in an information entity can mean different things for different types of information. For example, for assertions this reflects the confidence an agent has that the proposition it puts forth is true. For things like data items, it reflects the confidence an agent has that the data accurately reflects the aspect of reality its was intended to measure. has_confidence_level A relation between an agent and an other agent, typically an organization, on whose behalf a Contribution is made. performed_on_behalf_of performed_for A relation between one entity and an informtion content entity that provides a description of it. Consider: http://semanticscience.org/resource/SIO_000557 ! 'is described by' is_described_by contributesTo A relation between an agent and an entity toward which the agent made a contribution. contributes_to A relation that directly connects an assertion and an evidence item that contributes to one or more of its evidence lines. This evidence provided by this item may support or dispute the target assertion. assertion_has_evidence_item has_evidence_information has_evidence_line_with_item This relation can be used to link an assertion directly to evidence items that support it. Evidence items are typically organized into 'evidence lines' that group them according to the argument(s) to which they contribute. This shortcut relation supports use cases where it is desirable to elide over this level of organization and create direct links from an assertion to the fundamental pieces of information that represent evidence supporting it. A property chain (has_evidence_line o has_evidence_item -> has_evidence_with_item) is defined that can be used to infer this direct edge, facilitating interoperability between data sets that do and don't implement evidence lines to organize evidence items. has_evidence A relationship that holds between an assertion and a term that summarizes its asserted conclusion. asserted_outcome assertedConclusion asserted_conclusion Deprecate until there is a specific use case requiring this relation. obsolete_has_quantifier true A relation that holds between a study finding and a data item it describes (i.e. a data item generated by the study whose results are described by the finding). describes_supporting_data describes_study_data A relation that holds between a statement or proposition which can be captured in part or in whole as a directional relationship between two entities, and the entity that representing the subject of this relationship. has_subject A relation that holds between a statement or proposition which can be captured in part or in whole as a directional relationship between two entities, and the property serving as the predicate in this relationship. has_predicate A relation that holds between a statement or proposition which can be captured in part or in whole as a directional relationship between two entities, and the entity that representing the object or value of this relationship. has_object A shortcut relation that links an assertion directly to a term representing the type of evidence that supports it. true Relation expands to has_evidence_line o rdf:type -> has_evidence_type has_evidence_of_type ExploratoryObjectProperty A relation describing the quality of a piece of information, wich may or may not be used as evidence by an agent making an assertion. This property is used to indicate the inherent quality of a piece of data, based on the rigor of the experiment that produced it. It is not a direct indicator of the strength of evidence the data may provide for an assertion. The value of this property is typically a term from some defined set of values that enumerates categorical degrees of quality (e.g. the CIViC five star 'trust rating' scale) Different systems or applications can create terms representing the levels of quality they wish to define for their use case. information_quality evidence_for is_evidence_line_for A relationship between an information resource found in some information system, and the agent (person, organization, computational agent) who is responsible for sharing/providing it to that information system. Consider: pav:providedBy Note that this property connects a resource to an agent, not to some other information resource from which it came (e.g. another database or an API from which the resource in question was obtained). Use the 'source' property to capture this type of relationship. provided_by A relation used to link an assertion or proposition to a source where supporting evidence for it was found (i.e. a document, document part, database, etc) has_supporting_evidence_from_source A relation used to link an assertion or proposition to a source where disputing evidence for it was found (i.e. a document, document part, database, etc) has_disputing_evidence_from_source A relation that directly connects an assertion and a piece of information that contributes to an evidence line interpreted to support the truth of the assertion. has_supporting_evidence A relation that directly connects an assertion and a piece of information that contributes to an evidence line interpreted to dispute the truth of the assertion. has_disputing_evidence Links an entity to a document that describes it. reference executes Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents. This property is defined by OBAN to specifically link 'associations', which are proposition-level entities, to their object (sensu RDF). It is therefore a more specific relation than its has_object parent, which can be used to link a statement or proposition to its object. association has object Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents. This property is defined by OBAN to specifically link 'associations', which are proposition-level entities, to the property representing the predicate of the reified triple. It is therefore a more specific relation than its has_predicate parent, which can be used to link a statement or proposition to its predicate. association has predicate Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents. This property is defined by OBAN to specifically link 'associations', which are proposition-level entities, to their subject (sensu RDF). It is therefore a more specific relation than its has_subject parent, which can be used to link a statement or proposition to its subject. association has subject An agent that originated or gave existence to the work that is expressed by the digital resource. The author of the content of a resource may be different from the creator of the resource representation (although they are often the same). See pav:createdBy for a discussion. pav:authoredBy is more specific than its superproperty dct:creator - which might or might not be interpreted to also cover the creation of the representation of the artifact. The author is usually not a software agent (which would be indicated with pav:createdWith, pav:createdBy or pav:importedBy), unless the software actually authored the content itself; for instance an artificial intelligence algorithm which authored a piece of music or a machine learning algorithm that authored a classification of a tumor sample. The date of authoring can be expressed using pav:authoredOn - note however in the case of multiple authors that there is no relationship in PAV identifying which agent contributed when or what. If capturing such lineage is desired, it should be additionally expressed using PROV relationships like prov:qualifiedAttribution or prov:wasGeneratedBy. Authored by SEPIO creates this relation distinct from existing PAV and PROV relations (e.g. pcav:createdBy), which are too specific about whether a relation refers to the agent who created the abstract information content, vs who serialized and documented in concrete form. http://purl.org/dc/terms/creator An agent primary responsible for making the digital artifact or resource representation. This property is distinct from forming the content, which is indicated with pav:contributedBy or its subproperties; pav:authoredBy, which identifies who authored the knowledge expressed by this resource; and pav:curatedBy, which identifies who curated the knowledge into its current form. pav:createdBy is more specific than its superproperty dct:creator - which might or might not be interpreted to cover this creator. For instance, the author wrote 'this species has bigger wings than normal' in his log book. The curator, going through the log book and identifying important knowledge, formalizes this as 'locus perculus has wingspan > 0.5m'. The creator enters this knowledge as a digital resource in the knowledge system, thus creating the digital artifact (say as JSON, RDF, XML or HTML). A different example is a news article. pav:authoredBy indicates the journalist who wrote the article. pav:contributedBy can indicate the artist who added an illustration. pav:curatedBy can indicate the editor who made the article conform to the news paper's style. pav:createdBy can indicate who put the article on the web site. The software tool used by the creator to make the digital resource (say Protege, Wordpress or OpenOffice) can be indicated with pav:createdWith. The date the digital resource was created can be indicated with pav:createdOn. The location the agent was at when creating the digital resource can be made using pav:createdAt. Created by Specifies an agent specialist responsible for shaping the expression in an appropriate format. Often the primary agent responsible for ensuring the quality of the representation. The curator may be different from the author (pav:authoredBy) and creator of the digital resource (pav:createdBy). The curator may in some cases be a software agent, for instance text mining software which adds hyperlinks for recognized genome names. The date of curating can be expressed using pav:curatedOn - note however in the case of multiple curators that there is no relationship in PAV identifying which agent contributed when or what. If capturing such lineage is desired, it should be additionally expressed using PROV relationships like prov:qualifiedAttribution or prov:wasGeneratedBy Curated by Derived from a different resource. Derivation conserns itself with derived knowledge. If this resource has the same content as the other resource, but has simply been transcribed to fit a different model (like XML -> RDF or SQL -> CVS), use pav:importedFrom. If a resource was simply retrieved, use pav:retrievedFrom. If the content has however been further refined or modified, pav:derivedFrom should be used. Details about who performed the derivation (e.g. who did the refining or modifications) may be indicated with pav:contributedBy and its subproperties. Derived from The original source of imported information. Import means that the content has been preserved, but transcribed somehow, for instance to fit a different representation model by converting formats. Examples of import are when the original was JSON and the current resource is RDF, or where the original was an document scan, and this resource is the plain text found through OCR. The imported resource does not have to be complete, but should be consistent with the knowledge conveyed by the original resource. If additional knowledge has been contributed, pav:derivedFrom would be more appropriate. If the resource has been copied verbatim from the original representation (e.g. downloaded), use pav:retrievedFrom. To indicate which agent(s) performed the import, use pav:importedBy. Use pav:importedOn to indicate when it happened. Imported from The URI where a resource has been retrieved from. The retrieving agent is usually a software entity, which has done the retrieval from the original source without performing any transcription. Retrieval indicates that this resource has the same representation as the original resource. If the resource has been somewhat transformed, use pav:importedFrom instead. The time of the retrieval should be indicated using pav:retrievedOn. The agent may be indicated with pav:retrievedBy. Retrieved from The resource is related to a given source which was accessed or consulted (but not retrieved, imported or derived from). This access can be detailed with pav:sourceAccessedBy and pav:sourceAccessedOn. For instance, a curator (pav:curatedBy) might have consulted figures in a published paper to confirm that a dataset was correctly pav:importedFrom the paper's supplementary CSV file. Another example: I can access the page for tomorrow weather in Boston (http://www.weather.com/weather/tomorrow/Boston+MA+02143) and I can blog ‘tomorrow is going to be nice’. The source does not make any claims about the nice weather, that is my interpretation; therefore the blog post has pav:sourceAccessedAt the weather page. Source accessed at Web address of the resource has_url SEPIO creates a relation separate from existing PAV and PROV relations (e.g. pav:createdOn) which are too specific about whether a relation refers to the date on which the abstract information content was created, or when it was serialized and documented as a concrete digital artifact or resource with a particular format. created_on Consider: 1. http://purl.org/dc/terms/created 2. http://purl.org/pav/createdOn ! Created on Def: The date of creation of the resource representation. The agents responsible can be indicated with pav:createdBy. This property is normally used in a functional way, indicating the time of creation, although PAV does not formally restrict this. pav:lastUpdateOn can be used to indicate minor updates that did not affect the creating date. 3. prov:generatedAtTime: The time at which an entity was completely created and is available for use. obsolete_date_created true The date that a particular resource or artifact was last modified or updated. date_last_updated http://purl.org/dc/terms/modified ! Date Modified Definition: Date on which the resource was changed. Examples of modification include adding or removing content to/from a document, updating information in a data record, fixing errors in a manuscript, etc. The important thing is that the modification retains the identity of the artifact. date_modified The date that a particular resource or artifact was last evaluated - typically to assess its quality, completeness, accuracy, conformance, etc. Evaluating an artifact does not involve its modification - however the suggestion of alterations can be a separate outcome of an evaluation. If the artifact is modified by the agent during or subsequent to the evaluation, this date can be captured using the date_modified property. date_evaluated The date that a particular resource or artifact was formally submitted to be reviewed and/or included in some larger resource (e.g. database, registry, collection, etc.). http://purl.org/dc/terms/dateSubmitted date_submitted Consider: http://www.w3.org/ns/prov#startedAtTime start_date date_created_before Relation between a report and a string of text that it contains has_textual_part A relation holding between an information content entity and the date on which the information it expresses was initially generated. Consider http://purl.org/pav/authoredOn date_authored occurredAtTime process_date time_of_activity activity_date Consider: http://www.w3.org/ns/prov#endedAtTime end_date Consider: http://purl.org/pav/curatedOn Definition: The date this resource was curated. pav:curatedBy gives the agent(s) that performed the curation. This property is normally used in a functional way, indicating the last curation date, although PAV does not formally restrict this. The value is of type xsd:dateTime, for instance "2013-03-26T14:49:00+01:00"^^xsd:dateTime. The timezone information (Z for UTC, +01:00 for UTC+1, etc) SHOULD be included unless unknown. If the time (or parts of time) is unknown, use 00:00:00Z. If the day/month is unknown, use 01-01, for instance, if we only know September 1983, then use "1983-09-01T00:00:00Z"^^xsd:dateTime. obsolete_date_curated true Consider: http://purl.org/pav/lastUpdateOn date_updated The date that a particular resource or digital artifact was formally validated as meeting some standard for quality, completeness, relevance, etc.. date_validated A quantitative value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about. This property has a similar intent as assertion_confidence_level, but used for quantitative numerical values. The 'confidence score' property does not only include statistical measures such as p-values that explicitly indicate a level of confidence. It also includes any quantitative score against which a threshold for making an assertion is defined - where the distance of this score from this threshold can be interpreted as an indicator of how much confidence we might have that the asserted conclusion is true. For example, many silico prediction tools such as SIFT interrogate biological sequence data to calculate a score that reflects the likelihood that a particular sequence variant negatively impacts gene product function. A variant is interpreted to be 'Tolerated', 'Damaging', or 'Deleterious' based on how its score compares against pre-defined thresholds. Here, we may have less confidence that a variant with a score just above the 'Damaging' threshold is truly damaging, versus a variant whose score is well above the threshold. has_confidence_score A relation used to link a statement to some quantitative measure about the statement itself (e.g. a confidence score) statement quantifier A relation used to qualify the meaning of a statement. Most commonly used with a "NOT" value to negate a statement - i.e. indicate that the claim implied by its strucuted representation is not true. For example, the negation qualifier on the following OBAN-style association would make the claim that BRCA2 is NOT linked to the phenotype 'abnormal lymphocyte count': <:assertion1> a OBAN:association; OBAN:association_has_object HP_0040088 (abnormal lymphocyte count); OBAN:association_has_predicate RO:0002200 (has_phenotype); OBAN:association_has_subject HGNC:1101 (BRCA2); SEPIO:0000346(quallifier) "NOT". statement qualifier date_created_after probabilistic quantifier A numerical value that quantifies the strength of evidence provided by a line of evidence. This is a counterpart to the evidence_line_strength object property - for use when the strength of evidence is captured using a quantitiative score/measure. evidence_line_strength_score occurred_in process_location activity_location ExploratoryDataProperty ObsoleteDataProperty true Date that a particular representation/manifestation of an information content entity was created - e.g. as a web resource or digital artifact. To describe the date that the information content carried by a digital artifact or resource as generated, use the 'date_authored' property. date_created http://www.w3.org/ns/prov#value 'This property serves the same purpose as rdf:value, but has been reintroduced to avoid some of the definitional ambiguity in the RDF specification (specifically, 'may be used in describing structured values'). The editor's definition comes from http://www.w3.org/TR/rdf-primer/#rdfvalue' has_value A point or period of time associated with an event in the lifecycle of an information entity or resource. Consider: http://purl.org/pav/contributedOn date identifier doi digital object identifier (doi) The version number of a resource. This is a freetext string, typical values are "1.5" or "21". The URI identifying the previous version can be provided using prov:previousVersion. This property is normally used in a functional way, although PAV does not formally restrict this. version A name for some thing. name BFO:0000001 entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) BFO:0000002 continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] BFO:0000003 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] 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] BFO:0000004 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]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant 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] BFO:0000015 process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. 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] 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] BFO:0000016 disposition BFO:0000017 realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable 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] BFO:0000019 quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] BFO:0000020 sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] characteristic specifically dependent continuant https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 We should name the inverse in COB and avoid the confusing inverse(..) construct b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] BFO:0000023 role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] BFO:0000031 gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] BFO:0000034 function BFO:0000040 material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] BFO:0000182 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 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 part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. CARO:0000000 Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. anatomical entity CARO:0000000 A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. CAROC:Brownsville2014 COB:0000077 action specification COB:0000082 A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. planned process COB:0000119 OBI:0000067 evaluant role COB:0000120 http://purl.obolibrary.org/obo/IAO_0000015 Pier 'representational entity' This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc information representation COB:0000121 http://purl.obolibrary.org/obo/IAO_0000109 measurement datum COB:0000122 physical information carrier ERO:0001716 A database is an organized collection of data, today typically in digital form. http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Database database A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. molecular function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. molecular_function GO:0003674 A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. GOC:pdt A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. jl 2012-09-19T15:05:24Z Wikipedia:Biological_process biological process physiological process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process GO:0008150 A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt true Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. Reactome:R-HSA-6788855 Reactome:R-HSA-6788867 phosphokinase activity GO:0016301 Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. kinase activity GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. ISBN:0198506732 Reactome:R-HSA-6788855 FN3KRP phosphorylates PsiAm, RibAm Reactome:R-HSA-6788867 FN3K phosphorylates ketosamines IAO:0000005 objective specification IAO:0000013 journal article Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. a report that is published in a journal person:Alan Ruttenberg person:Chris Stoeckert OBI_0000159 group:OBI journal article IAO:0000027 data item Data items include counts of things, analyte concentrations, and statistical summaries. 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/ PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item 1 IAO:0000030 information content entity - Data Items: A '548.5 mg/dl' measurement of blood glucose in mutant mice. - Protocols: A blood glucose assay protocol that describes how the measurement was taken. - Calculations: A 1.3951e-24 p-value statistic indicating a significant increase relative to wild-type mice. - Assertions: An assertion stating that "Lpr1 leptin receptor mutations can lead to diabetes". - Publications: A journal article that publishes this assertion. - Figure/Tables: A figure or table from this article that present data supporting it. - Software/Algorithms: A text-mining algorithm that mines the literature to identify and extract the assertion. - Databases: The MGI (Mouse Genome Informatics) database that stores the assertion as a structured gene-disease annotation. A generically dependent continuant that is about some thing. ICEs are abstract entities that convey information about things in the world. ICEs represent the information encoded in physical artifacts such as photographs, books, or digital storage medium (as opposed to the physical medium itself). A particular ICE can be encoded simultaneously in many physical or digital mediums and formats. For example, only one instance of the first edition of "War and Peace" exists as an ICE, representing information conveyed in this work. But many instances of "War and Peace" exist at the level of their physical concretizations in printed books or digital devices. Pier: 'data, information or knowledge'. OR 'representation information information content entity IAO:0000033 directive information entity IAO:0000064 A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. algorithm IAO:0000078 curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification IAO:0000088 report Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record) 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. 2009-03-16: work has been done on this term 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. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification PERSON: Alan Ruttenberg PERSON: Melanie Courtot PERSON:Chris Stoeckert GROUP: OBI OBI_0000099 report IAO:0000100 data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set IAO:0000102 data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part IAO:0000104 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. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg method plan specification plan specification IAO:0000109 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,}. 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 IAO:0000225 obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification IAO:0000306 A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions MHB: A figure depicting a tabular representation of data, typically created to highlight a particular aspect or view of a larger data set. They may include derived statistical measures summarizing the primary data. The concept described here represents a tables generated for purposes of documentation or publication of results, as opposed to database tables defined as structures for primary storage of source data in some information system. table IAO:0000308 figure Any picture, diagram or table An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. PERSON: Lawrence Hunter MHB: A figure is a graphical presentation of information created as a vehicle to share with an audience, e.g. in a publication or report. Figures may include raw and/or summarized/derived data, or diagrammatic abstractions of results, conclusions, or hypotheses. Figures often present data in a form that is summarized or abstracted for human consumption, using graphical conventions that may sacrifice detail of underlying data for ease or understanding. figure IAO:0000310 document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document IAO:0000311 publication A journal article or book A document that has been accepted by a publisher PERSON: Lawrence Hunter publication IAO:0000313 patent US Patent 6,449,603 A document that has been accepted by a patent authority PERSON: Lawrence Hunter patent IAO:0000409 denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type OBI:0000011 planned process Injecting mice with a vaccine in order to test its efficacy A processual entity 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.) 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) completely executed planned process planned process OBI:0000066 a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). investigation OBI:0000070 assay OBI:0000175 p-value A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. May be outside the scope of OBI long term, is needed so is retained PERSON:Chris Stoeckert WEB: http://en.wikipedia.org/wiki/P-value p-value OBI:0000235 standard error A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution. person:Chris Stoeckert group:OBI see P-Value standard error OBI:0000260 plan OBI:0000272 PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. experimental protocol protocol OBI:0000338 drawing a conclusion based on data Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion PERSON: Bjoern Peters PERSON: Jennifer Fostel Bjoern Peters drawing a conclusion based on data OBI:0000938 OBI:0001146 binding assay Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen.nnThe following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture. An assay with the objective to characterize the disposition of two or more material entities to form a complex. PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum binding assay OBI:0002165 protein localization assay An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied. Rebecca Tauber OBI development call protein localization assay A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATO:0000001 quality PATO:0000001 A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG SEPIO:0000000 The proposition that BRCA1:2685T>A causes familial breast cancer. An abstract entity representing the sharable meaning of what is expressed in a particular assertion. In the SEPIO model, an assertion is akin to an act in speech or text that expresses beleif in the truth of a proposition. It is the proposition that represents the semantic content of a claim, and bears truth value. Mappings to terms from related models: 1. http://purl.org/see/rdo#proposition A SEPIO proposition is equivalent to a 'proposition' from the Semantic EvidencE framework. "The class rdo:proposition represents propositions i.e. the sharable objects of propositional attitudes like belief or desire and the bearers of truth values. As truth bearers they are either true or false. They are taken to represent the semantic content of sentences or larger lexical entities formulated in some natural or artificial language.") 2. http://purl.org/mp/Holotype The notion of a holotype from the Micropublications model is related to a SPEIO proposition - in that it represents a statement that is selcted to all other statements expressing the same meaning. 3. http://purl.org/oban/association An OBAN proposition is a more type of proposition, that is structured/expressed according to the specifications laid out in the OBAN ontology. http://plato.stanford.edu/entries/propositions The notion of a proposition, and its relationship to an assertion, derives from the domain of logic and philosophy [12]. Propositions are abstract entities that, like numbers, are independent of space and time. They represent only the meaning that is expressed in a particular agent’s assertion, and are ‘sharable’ in that the same proposition can be expressed in many different assertions. Propositions are primary bearers of truth value, in that they are true or false. From http://plato.stanford.edu/entries/propositions/: "Propositions are the sharable objects of the attitudes and the primary bearers of truth and falsity. This stipulation rules out certain candidates for propositions, including thought- and utterance-tokens, which presumably are not sharable, and concrete events or facts, which presumably cannot be false." proposition SEPIO:0000001 The following are three seperate assertion instances, that assert the same proposition (that BRCA1:2685T>A causes familial breast cancer) 1. Counsyl's assertion on October 5, 2009 that BRCA1:2685T>A causes familial breast cancer. 2. The ENIGMA consortium’s assertion on September 18, 2010 that BRCA1:2685T>A causes familial breast cancer. 3. A later assertion by the ENIGMA consortium on May 9, 2013, based on new evidence, that BRCA1:2685T>A causes familial breast cancer. A statement made by a particular agent on a particular occasion that a particular proposition is true, based on the evaluation of one or more lines of evidence. SEPIO distinguishes two high-level subtypes of statements: 1. Findings are statements that report the immediate, objective results of an experiment, observation, or study - without bias or interpretation. A finding statement results simply from the act of reporting or summarizing these direct observations, calculations, or measurements. 2. Assertions, by contrast, result from acts of interpretation and/or inference, based on information used as evidence. The statement here is a conclusion drawn from critical evaluation of this more foundational information, and its validity depends on the quality of this information and the act of interpretating as evidence. claim evidence-based assertion propostional assertion Derived from http://purl.org/see/rdo#assertion The identity of a particular assertion is dependent upon (1) what it claims to be true (its semantic content, aka its ‘proposition’), (2) the agent asserting it, and (3) the occasion on which the assertion is made. Many agents can make assertions expressing belief in the same proposition (e.g. ENIGMA’s assertion that that BRCA1:2685T>A causes familial breast cancer is a separate instance than Counsyl’s assertion of the same underlying proposition). Likewise, a single agent can make more than one assertion of belief in the same proposition on different occasions (e.g. ENIGMA may make a separate assertion of the same proposition that BRCA1:2685T>A causes familial breast cancer at a later date, based on additional evidence). Assertions as defined in SEPIO are the result of some logical inference made based on the interpretation of evidence. They put forth a proposition that may or may not be true - the validity of which ultimately rests on the quantity, quality, diversity, and concordance of evidence supporting it. Statements directly reporting study results or observations are not considered assertions in this sense, as they merely report what was observed or recorded, but do not rely on a leap of logical inference (see 'study finding'). assertion SEPIO:0000002 An example of an evidence line would be the argument that a finding such as "Lepr1 KO mice exhibit lower blood glucose levels than matched WT controls" makes in support of the proposition that "Lepr1 gene is involved in diabetes". The Evidence Items supporting this line of evidence could include experimental data from a study exploring blood glucose levels in Lepr1 KO mice, such as a 548.5 mg/dl measurement of blood glucose in a Lepr<tm1b/tm1b> mutant mouse, or a 1.3951e-24 p-value indicating this measure to be significantly different from wild-type mice. Here, the finding and its supporting data exist independently of their use as evidence. An evidence line based on this finding comes into existence only when an agent interprets this finding as providing a meaningful argument for a particular proposition, in the act of making an assertion. (This example is based on data from the IMPC record here: http://bit.ly/2t4J1TI) An evidence line represents an independent and meaningful argument for or against a particular proposition, that is based on the interpretation of one or more pieces of information as evidence. evidence-based argument An evidence line is created through the interpretation of one or more pieces of information that collectively support a meaningful argument for or against a proposition. To qualify as an Evidence Line, this argument must be independently significant as evidence - i.e. it must be capable of affecting the probability of accepting the target proposition as true. This does not mean, however, that it is independently sufficient to establish belief in the proposition, as additional evidence lines may be required to ultimately accept the proposition as true. For example, in the ACMG framework for variant interpretations establishes "absence in population databases" as a type of evidence line that can argue for the pathogenicty of a particular variant. But this argument alone is not considered sufficient to establish a variant's pathogencity, as the other types of evidence are additionally required to establish the truth of this Proposition (e.g. a line of evidence demonstrating the variant to have a deleterious effect on protein function, or showing it to segregate with disease features in a family tree). evidence line SEPIO:0000003 An act of interpreting evidence to make an assertion of belief that a particular proposition is true Mappings to terms from related models: Likely equivalent to http://purl.org/see/rdo#act_of_inference. May be equivalent to http://purl.obolibrary.org/obo/ECO_0000217 ! assertion method. act of assertion An assertion process includes the processes of interpreting data and evaluating it as evidence for the validity of a proposition. They are affected by a particular agents on a particular occasions, and can be specified by assertion methods or guidelines. assertion process SEPIO:0000004 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 SEPIO:0000037 A directive information entity that specifies an algorithm or heuristics for evaluating evidence in the process of making an assertion. SEPIO implements several OWL individuals representing instances of commonly applied assertion methods, primarily those used in pathogenic variant classification such as the ACMG variant classification criteria. Assertion methods can be informal guidlines or heuristics that support manual evaluation of evidence, e.g. the ACMG Variant Classification Guidelines. Assertion methods can also be formally encoded as algorithms that allow computational or statistical analysis of data as evidence in support of making an assertion - e.g. multifactorial analysis algorithms that operate on specified data to generate a quantitative score indicating the validity of a particular proposition. assertion method SEPIO:0000048 A role borne by a person, group, organization, or information processing entity (e.g. software, algorithms) in virtue of its active participation in a process leading to some outcome (e.g the generation, modification, or provision of some entity). A role realized by a participant in a process such that the participant causes the process. agent role http://purl.org/see/rdo#agent_role In the context of evidence and proveannce, agents are persons, groups, organizations, or software that are responsible for making assertions or generating the evidence and data that support them. agent role contributor role SEPIO:0000049 A role inhering in any material or information artifact that is used by an agent as specified input into a planned process. In the context of evidence and provenance for scientific claims, resources are entities that are used by agents to facilitate processes aimed at the generation of assertions or the evidence and data that support them. Examples include instruments, reagents, model systems, software, and protocols. resource role SEPIO:0000055 Mappings to related terms: 1. http://purl.obolibrary.org/obo/ECO_0000218 ! manual assertion ECO Definition/Comment: A manual assertion could be based on evidence that is generated by and interpreted by a human or it could involve human review of computationally generated information. obsolete_manual assertion process true SEPIO:0000056 An assertion process performed through algorithmic analysis by a computational agent, independent of human review. Mappings to related terms: 1. http://purl.obolibrary.org/obo/ECO_0000203 ! automatic assertion ECO Definition/Comment: An automatic assertion is based on computationally generated information that is not reviewed by a person prior to making the assertion. For example, one common type of automatic assertion involves creating an association of evidence with an entity based on commonness of attributes of that entity and another entity for which an assertion already exists. The commonness is determined algorithmically. Ultimately even automated assertions require a human agent to set a confidence threshhold that determines when a computational output (e.g. a sequence similarity p-value) justifies an assesrtion being made. obsolete_automated assertion process true SEPIO:0000058 The process history leading to the creation and current condition of an artifact. Consider whether it is appropriate to place this under the BFO:history class, which may apply only to histories of "material entities or sites". And consider if we want/need to define this class at all - as it is not used to model data - only as a means to record what SEPIO considers provenance to be, and how it is different from evidence. For scientific assertions/claims, this is the process history leading to the asseertion being made, including processes through which evidence is evaluated, and processes through which information used as evidence is created. The transitive nature of provenance means that the provenance history of informtion used as supporting data becomes provenance for an assertion that uses this information as evidence. Provenance metadata describes these processes, including accounts of who conducted these processes, what entities participated in them, and when/where they occurred. provenance SEPIO:0000066 A study that involves primary research of subjects or specimens in a natural, cliniclal, or laboratory setting. primary research study SEPIO:0000067 Formal clinical study performed using cohorts of multiple patients clinical study SEPIO:0000069 http://purl.org/net/OCRe/research.owl#Interventional_study interventional clinical study SEPIO:0000070 http://purl.org/net/OCRe/research.owl#Observational_study observational clinical study SEPIO:0000071 http://purl.org/net/OCRe/research.owl#Case_control_study case-control clinical study SEPIO:0000072 A research dtudy perfomred using an experimental model system such as a cell line, or model organism. experimental model study SEPIO:0000073 in vitro study SEPIO:0000074 in vivo study SEPIO:0000076 cell-based in vivo study SEPIO:0000077 tissue-based in vivo study SEPIO:0000078 whole organism in vivo study organism-based in vivo study SEPIO:0000079 A study based only on analysis of existing data, as found in artifacts such as community/curated databases, raw datasets, or publications. data-driven study secondary research study SEPIO:0000080 A curation-based study that uses only one or more literature publication as input data source. Based on ClinVar 'literature only' collection method: "for submissions that provide the interpretation of a variant from one or more publications. No additional curation has been performed by the submitter; the interpretation is from the publication(s) only." literature-based study SEPIO:0000081 Based on Clinvar 'curation' collection method: "for variants that were not directly observed by the submitter, but were interpreted by curation of multiple sources, including clinical testing laboratory reports, publications, private case data, and public databases." curation-based study SEPIO:0000102 A study based on analysis of data gathered from baseline studies of a population group of apparently unaffected individuals to assess allele frequencies ClinVar reference population data study SEPIO:0000125 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 SEPIO:0000127 A group of individuals (organisms, specimens, samples) that are subjects in an observational or intervention study, and whose members represent experimental replicates as defined in a study design by the same independent variable specifications (i.e. subjected to the same selction criteria or set of experimental interventions). Consider: STATO_0000193, OBI_0000174 obsolete_study group true SEPIO:0000131 A planned process in which existing data is collected, organized, and improved in preparation for subsequent use. curation SEPIO:0000133 A data item that quantifies the degree of support an agent believes an evidence line to provide for a particular proposition. Consider also framing as categorical measurement values?: A categorical measurement reflecting an agent's cognitive quantification of the degree of support (s)he believes an evidence line to provide for a particular proposition. The strength of a line of evidence typically depends on the *type* and *quality* of the study(ies) that generate its supporting evidence items. 1. Type of Study: In a particular domain of research, certain types of studies are commonly held to produce data that is more meaningful and reliable than others, as evidence for a particular type of assertion. These more reliable studies tend to draw on experimental systems that more accurately replicate the natural phenomenon being studied, and experimental designs that reduce confounding variables and biases. For example, in vivo studies of gene function provide stronger evidence than in vitro systems that may not replicate all aspects of the biology of a living system, and randomized controlled clinical trials are held to be more reliable than retrospective or case control studies that are more susceptible to confounding factors. 2. Quality of Study: A given study can be performed to varying degrees of rigor and comprehensiveness, irrespective of the type of study it represents. This is another important factor in assessing the overall strength of evidence it may produce. Higher quality studies will have carefully defined controls, and be replicated numerous times to ensure reproducibility. Other factors that are often used as secondary indicators of the quality of research data include the quality of the journal in which it is published, and the reputation of the lab or institution performing the study. In SEPIO, the notion of evidence quality is captured in an attribute separate from the notion of evidence strength. And the notion of study type can be represented in the type assigned to a study instance, or the evidence code used to type an evidence line (which are often based on the type of study that produced the evidence data). Evidence strength typically relies on assessment of one or both of these more fundamental attributes of evidence. evidence strength SEPIO:0000143 A study that documents observations or findings from a single patent. case reporting patient case study SEPIO:0000148 evidence role SEPIO:0000149 - the raw count data from a case-control study comparing the frequency of an allele in two cohorts or populations - the calculated p-value as a measure of statistical significance of the difference identified in the study - a published figure documenting these data - an author statement summarizing the outcomes of the study (i.e. a 'study finding') - a broader conclusion inferred from interpretation of the data reported in a study (i.e. an evidence-based 'assertion') An information content entity that is used as evidence to evaluate the validity of a target assertion or proposition. evidence evidence information 'Evidence Item' is a broad term covering any information interpreted as evidence in the act of making an assertion. Classes representing different types of evidence items are imported here from ontologies such as OBI, IAO, and STATO, and include: - measured data values - derived data values such as statistical calculations and confidence measures - figures presenting or describing such data - author statements representing summaries of or conclusions drawn from such data - established facts in a field of research Note that publications and reports are considered separately from 'evidence items', as a they *contain* information (data values, figures author statements) that can be used as evidence. But on its own a publication or report is merely a proxy for this information. evidence item SEPIO:0000153 creator role SEPIO:0000154 assessor role SEPIO:0000155 validator role approver role SEPIO:0000156 curator role SEPIO:0000157 obsolete software agent true 1 SEPIO:0000158 The actions taken by a particular agent in the creation, modification, assessment, or deprecation of an artifact. This concept is similar in meaning and usage to PROV:Attribution. Consider aligning or adopting. Contribution instances organize information about who, when, where, how (e.g. what roles were played), and on whose behalf these actions were performed. The scope of a Contribution instance includes only the actions of a single agent in contributing to a particular artifact - which may be performed in one continuous effort, or multiple discrete sessions of work. The contributing agent can be a single individual, or an organization of multiple individuals acting together. contribution SEPIO:0000173 Findings statements tend to take the form of "We observed that . . . ", or "Assay X revelaned that . . . ", or "X was determined to be Y in a study of . . . ". For example: "Smith et. al observed that a positive response to imatinib treatment was two-fold higher in a cohort of leukemia patients bearing Bcr-Abl fusions compared to those lacking this driver mutaiton." A statement summarizing the outcome of a sequencing analysis: "DNA sequencing data from patient X revealed an A->T mutation at position 2143 in gene Y". A statement summarizing the outcome of a variant population frequency study: "The frequency of variant X was determined to be 0.00015 in a cohort of non-finnish european subjects described in the ExAC dataset." A statement describing the immediate results of a research study, describing what was directly observed, measured, or derived through mathematical calculation. In SEPIO, a high-level distinction is made between statements that are 'findings' vs 'assertions'. Findings are statements that report/summarize what was directly observed or calculated in a study, and are about only the immediate participants in the experiment or study. As such, findings involve no interpretation or inference from the data to draw broader conclusions. Assertions, by contrast, are statements that derive from some degree of interpretation or inference based on the evaluation of 'evidence', and often make broader claims about the types or categories to which study participants belong. This distinction is important because the provenance and validity of a 'finding' statement does not depend on subjective interpretation of 'evidence' in the same way that of an assertion does. This has modeling implications for how findings and assertions are linked to information that supports them. In practices, instances of 'study findings' are used to group one or more data items from a particular research study that are relevant as evidence for an assertion. The utility of this class is in allowing the shared provenance of these data items to be more efficiently represented - as things like agent, date, and methods can be described once for the data set and inferred to apply to all individual data items that comprise it. study outcome - While the act of generating a finding is simpler, it does involve some cognitive effort that could be guided by some method (i.e., one defining what experimental context should be included in the finding statement, and how this and the observed outcomes are reported). Which means that findings are not the direct output of an assay, which merely generates data. So perhaps in SEPIO we commit to only considering research processes at the level of studies - such that even assays would potentially involve some act of summarizing the results as a finding. - Note that at present 'study data sets' can serve the same 'organizational' purpose as 'study findings' - we should converge on one recommended way to perform this level of organization of evidence data. A study finding is a statement that summarizes the immediate results of a particular experiment or study. It describes only what was directly observed, measured, or calculated, and optionally the experimental context of these observations. It does not describe more general conclusions that may have been inferred from such results. As such, the scope of what a finding describes is limited to the direct participants in the study - i.e. it is about only the instances observed or measured in the study. It makes no broader inference or conclusion about types or classes to which these instances belong. This is not to say that the onserved findings are necessarily accurate or correct - only that they were indeed made in a particular study. For example, the finding that "Sequencing of DNA from patient X revealed an A->T mutation at position 2143 in gene Y" is a matter of fact - this was the outcome of the assay, even if the finding is an artifact of low sequencing coverage. Metadata about the finding (e.g. sequencing methods/reagents used, coverage or read depth) are recoded so users can judge for themselves whether the objectively reported finding accurtely reflects the biology it describes. SEPIO distinguishes two high-level subtypes of statements: 1. Findings are statements that report the immediate, objective results of an experiment, observation, or study - without bias or interpretation. A finding statement results simply from an act of reporting or summarizing these direct observations, calculations, or measurements. 2. Assertions, by contrast, result from acts of interpretation and/or inference, based on information used as evidence. The statement here is a conclusion drawn from critical evaluation of this more foundational information, and its validity depends on the quality of this information and its interpretation as evidence. study finding SEPIO:0000174 The following is derived from https://en.wikipedia.org/wiki/Statement_(logic): Examples of sentences that are (or make) statements: "Socrates is a man." "A triangle has three sides." "Madrid is the capital of Spain." "There are five ducks on the lake" "The BRAF V600E mutation causes breast cancer" Examples of sentences that are not (or do not make) statements: "Who are you?" "Run!" "Greenness perambulates." "I had one grunch but the eggplant over there." "The King of France is wise." "Broccoli tastes good." The first two examples are not declarative sentences and therefore are not (or do not make) statements. The third and fourth are declarative sentences but, lacking meaning, are neither true nor false and therefore are not (or do not make) statements. The fifth and sixth examples are meaningful declarative sentences, but are not statements but rather matters of opinion or taste. An information content entity expressing a declarative sentence that is either true or false. From https://en.wikipedia.org/wiki/Statement_(logic) (2017-06-21): "A statement is a declarative sentence that bears truth value, in that it can be either true or false. This definition derives from the domain of logic, where a statement is either (a) a meaningful declarative sentence that is either true or false, or (b) that which a true or false declarative sentence asserts. In the latter case, a statement is distinct from a sentence in that a sentence is only one formulation of a statement, whereas there may be many other formulations expressing the same statement . . . In (this treatment), "statement" is introduced in order to distinguish a sentence from its informational content. A statement is regarded as the information content of an information-bearing sentence. Thus, a sentence is related to the statement it bears like a numeral to the number it refers to. Statements are abstract logical entities, while sentences are grammatical entities." ---- Note that the definition in (b) describes something closer to the notion of a 'Proposition' as defined in SEPIO? Statements are sentences (or, more precisely, the information content of sentences) that declare a definitive or proposed fact - expressing something about the world or one's experience of it that may or may not be true. The identity of a particular Statement is dependent upon (1) what it reports as true (its semantic content), (2) the Agent stating it, and (3) the occasion on which the statement is made. The phrase "the pink elephant" describes an entity, but is not a 'statement' as it has no truth value. By contrast, the phrase "the pink elephant is in the room" is a statement as this can be evaluated for its truth. statement SEPIO:0000175 A statement describing something that was observed or recorded. In SEPIO, a high-level distinction is made between Statements that are 'Observations' vs 'Assertions'. Observations are statements that report what is observed, and are inherently true in the sense that they reflect an agents particular experience. Assertions are statements that derive from some degree of interpretation or inference based on the evaluation of 'evidence'. This distinction is important because the ultimate truth of observations or findings do not depend on evidence in the same way that the truth of assertions does. Accordingly, any data related to an observation is not treated as evidence, and captured as observations. An observation reflects only what an agent observed or device recorded. It is therefore considered a matter of fact, rather than a propositional assertion that may or may not be true. This does not mean that the observations or recordings were necessarily accurate or correct - only that they were indeed made by an agent. For example, the observation that "I counted six ducks in the pond" is a matter of fact, even if there are actually seven because I missed one that was hiding in the reeds. obsolete_observation true SEPIO:0000180 A statement (ie an assertion or finding) that is used as evidence to evaluate the validity of a target assertion or proposition. Term is confusing and not required for current use cases. Main reason it was creaated is that his term is used in efforts like CIViC, and we wanted to be clear about how it fits into the SEPIO model. But this can be accomplished in documentation outside of the ontology. Axioms: Eq: statement and (contributes_to_evidence_line some 'evidence line') Sc: 'information content entity' has_role some 'evidence role' Evidence Statements can be 'findings' that summarize data and outcomes from a particular study, or evidence-based 'assertions' that make a broader claim, as inferred from the interpretation and evaluation of previously generated information. obsolete_evidence statement true SEPIO:0000181 Research data, or a product derived from research data such as data sets or figures, that are used as evidence to evaluate the validity of a target assertion or proposition. Evidence data is not classified as a 'data item' because it is intended to cover products derived from data such as figures, tables, and data sets. evidence datum Term is confusing and not required for current use cases. Axioms: Eq: ('data item' or table or figure) and (contributes_to_evidence_line some 'evidence line') Sc: 'information content entity' has_role some 'evidence role' Instances of this class can include elemental 'data items' such as experimental measurements or derived statistical calculations or scores (e.g. a 548.5 mg/dl blood glucose level, or a 1.3951e-24 p-value), data sets containing several such values and possibly metadata about them, or tables/figures that render such data for human consumption. The notion of 'evidence data' is meant to be contrasted with the notion of an 'evidence statement', which is a statement used as evidence. (Statements here are logical sentences with truth value that are typically supported by interpretation of more fundamental data). obsolete_evidence data true SEPIO:0000185 A set of data arranged in rows and columns. http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C48693 ! Data Table Not required for data models. obsolete_data table true SEPIO:0000186 A study with the goal of assessing and documenting phenotypes exhibited by one or more patients. Source: ClinVar (" 'Phenotyping only' is intended for variants that are submitted to ClinVar to provide individual observations with detailed phenotype data, such as submissions from clinicians or patient registries, without an interpretation from the submitter. The interpretation from the testing laboratory may be provided in a separate field.") ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/release_notes/20170803_data_release_notes.pdf patient phenotyping study SEPIO:0000187 A measurement datum that quantifies the level of confidence an agent has that a particular piece of information is true. confidence level SEPIO:0000258 Source: ClinVar (" 'Provider interpretation' is intended for variants that were interpreted by a clinical provider. For example, the clinician may reclassify the variant using detailed patient phenotype information that was unavailable to the testing laborator") ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/release_notes/20170803_data_release_notes.pdf provider interpretation SEPIO:0000340 Organizational class that groups classes imported from the skos model to support creation and definition of value sets for particular SEPIO data model implementations. skos terms SEPIO:0000385 Consider IAO:0000104 (plan specification). plan specification Decided to use IAO:plan specification here. Will give this term 'method' as a SEPIO-preferred label. An information content entity that specifies instructions for how a particular objective can be achieved. obsolete_method true SEPIO:0000400 The set of data output from a study of the frequency of a particular allele in a particular population, which includes the following data (and metadata) items: { "ascertainment": "ExAc ascertainment method" "population": "Non-Finnish European" "allele": "CAR:CA011797", "alleleCount": 66706, "alleleNumber": 1, "alleleFrequency": 0.00001499, "homozygousAlleleIndividualCount": 0 } This collection of data may be described by, but remains distinct from, a 'study finding' statement that summarizes the results in narrative form. A data set comprised of data items produced by a single research study. Instances of this class are used in SEPIO to group one or more data items from a particular research study that are relevant as evidence for an assertion. The utility of this class is in allowing the shared provenance of these data items to be more efficiently represented - as things like agent, date, and methods can be described once for the data set and inferred to apply to all individual data items that comprise it. The data items comprising a study data set may include primary measurements, derived calculations, metadata about study participants and methods, or parameters of execution. 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. study data set SEPIO:0000401 A declarative sentence that expresses a belief or judgement that is not necessarily based on fact or knowledge. Opinions are matters of subjective judgement or taste, and typically not able to be scientifically validated as objectively true based on empirical evidence. In this way, they are distinct from statements that have inherent truth value. obsolete_opinion true SEPIO:0000402 A data item that indicates an agent's assessment of whether an evidence line supports or disputes a target proposition (or represents inconclusive evidence that is not sufficient for either). Consider also treating this as an attribute/quality of an evidence line: An attribute of an evidence line describing whether it supports or disputes a target proposition (or represents inconclusive evidence that is not sufficient for either). evidence direction SEPIO:0000414 A data item that indicates the quality of the data used as evidence by an agent making an assertion. The quality of an evidence item is a measure of the rigor applied in performing the study and anlysis tasks used to produce it. Higher quality studies will have carefully defined controls, and be replicated numerous times to ensure reproducibility. Other factors that are often used as secondary indicators of the quality of research data include the quality of the journal in which it is published, and the reputation of the lab or institution performing the study. Evidence qualitty is an important factor in assessing the overall strength of evidence it may produce. evidence quality SEPIO:0000431 Recommendations are another type of statement besides assertions that can be supported by evidence. They don't put forth a proposed facts as true, but instead describe a recommended action on the foundation of evidence that it will be beneficial. recommendation SEPIO:0000432 A hypothesis is another type of statement that, like an assertion, can be supported by evidence. It puts forward a possible fact as true, but does not express an agents belief in this fact. Rather, it is a possible fact whose truth will be explored via reasoning or experimentation. hypothesis SEPIO:000383 A document containing a collection of data or statements about some entity. SIO:000088 'Record' here is broadly defined to include any document holding (typically) structured information about a particular entity. This can include individual records from a database or knowledgebase that hold information about the subject of the record. Specific examples include: - A single row of a table in a relational database. - A JSON or XML document holding information describing some entity. - A VCF File describing varaints in a patient, or a single row in this VCF file describinng a particular variant. - A Uniprot knowldgebase record describing the BRCA2 protein (http://www.uniprot.org/uniprot/P51587) - A ClinVar knwoledgebase record describing an assertion about the pathogenicity of the NM_000059.3(BRCA2):c.10G>T variant (https://www.ncbi.nlm.nih.gov/clinvar/variation/51063/) - An EHR record for a hospital patient. record STATO:0000039 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 STATO:0000104 A z-score (also known as z-value, standard score, or normal score) is a measure of the divergence of an individual experimental result from the most probable result, the mean. Z is expressed in terms of the number of standard deviations from the mean value. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra https://controls.engin.umich.edu/wiki/index.php/Basic_statistics:_mean,_median,_average,_standard_deviation,_z-scores,_and_p-value#Z-Scores z-score STATO:0000184 A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s. obsolete_ratio true Associations are a form of proposition, framed as a tuple linking two (or more) entities through defined relationships. association oboInOwl:ObsoleteClass owl:Nothing owl:Thing skos:Concept An idea or notion; a unit of thought. Concept An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities. Activity An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity. prov:Agent is considered equivalent to foaf:Agent (http://xmlns.com/foaf/0.1/Agent ) Def = "The Agent class is the class of agents; things that do stuff. A well known sub-class is Person, representing people. Other kinds of agents include Organization and Group." Agents typically persons, organizations, or software that perform tasks, including making assertions, or generating information used as evidence. In the execution of such tasks, an 'agent role' is realized that inheres in the agent. Agent An organization is a social or legal institution such as a company, society, etc. Consider: http://xmlns.com/foaf/0.1/Organization Organization Person agents are people. Consider: http://xmlns.com/foaf/0.1/Person Person A software agent is running software. Software agents are autonomous computer programs that carries out tasks. They designed to execute algorithm(s) that receive some input information and direct its processing to achieve a specified goal. Artificial intelligence is not required to be considered a software agent - only that it can autonomously execute programmed tasks. SoftwareAgent foaf:Group The Group class represents a collection of individual agents (and may itself play the role of a Agent, ie. something that can perform actions). This concept is intentionally quite broad, covering informal and ad-hoc groups, long-lived communities, organizational groups within a workplace, etc. Some such groups may have associated characteristics which could be captured in RDF (perhaps a homepage, name, mailing list etc.). Group example to be eventually removed example to be eventually removed failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 out of scope An evidence direction indicating that an evidence line provides an argument that supports the validity of a target assertion. supporting disputing An evidence direction indicating that an evidence line lacks sufficient credibility, relevance, or completeness to argue for or against the validity of a target assertion. inconclusive 2023-06-13 has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part has part realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes realizes concretizes intended to realize realizes http://purl.obolibrary.org/obo/IAO_0000136 Is_about is a (currently) primitive relation that relates an information artifact to an entity. is about is_about 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 has participant mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". capable of capable of p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes 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. p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. Chris Mungall produces has output inverse of has output Chris Mungall output of A relationship between an assertion or proposition and an evidence line used in evaluating its validity. Consider re-use of http://purl.obolibrary.org/obo/RO_0002558 ! 'has evidence'. Definition = "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x." See also http://semanticscience.org/resource/SIO_000772 ! 'has evidence'. has_evidence has_evidence_line Consider use of http://purl.obolibrary.org/obo/RO_0002217 ! actively participates in. Definition = "actively participates in y if and only if x participates in y and x realizes some active role" has_agent A relation holding between an assertion and the proposition that it puts forth as true. Mapping to related terms: Consider: http://purl.org/see/rdo#is_assertion_asserting assertsProposition In practice, SEPIO recommends that data is captured at the assertion level, and post-processed as needed to aggregate assertions making the same claim under a single proposition using this property. asserts_proposition Consider RO:0000087 ! has_role (def = a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence). However, this property is defined as a relation between an independent continuant and a role. In BFO, dependent continuants (such as information) cannot bear roles. has_role A relation holding between an evidence line and an individual information entity that contributes to the argument it represents. has_supporting_information has_evidence_item As an example, consider the assertion that "Variant X causes Disease Y". At an abstract level this represents a bfo: information content entity (or frbr:Work). This abstract assertion can be concretized / encoded various formats - e.g. a free-text sentence, an rdf graph, a blob of json, or stanza of XML. Each such manifestation might use a different model or structure to represent this knowledge. Each such concrete form is considered a separate resource/digital artifact at the 'manifestation' level, but each expresses the same knowledge. The authored_by and date_authored properties allow us connect an abstract or concrete representation of this assertion to who and when the knowledge was originally generated. This will be the same agent and date for all formats/manifestations listed above. The created_by and date_created properties allow us to connect a representation of the abstract or concrete assertion to who and when the specific manifestation was created in a particular format. The agent/dates here will be different for each of the formats/manifestations listed above. A relation between an information content entity (or concrete manifestation of it as a particular resource/digital artifact), and the agent that originally generated the information content. Older note - remove before releasing: We intentionally avoid use of a more generic "creator" property here, as this term is used in established standards such as PAV and DC to specifically describe agents who generated a specific representation of an information content entity. For example, the pav:createdBy property is used specifically to describe agents contributing to a specific representation. SEPIO, by contrast, aims to describe the agent(s) responsible for generating the abstract information content these concretized artifacts express. For this reason, SEPIO creates the more specific "stated_by" relation to explicitly distinguish the act of making a statement (generating its information content) from the act of creating a specific digital representation of the statement (generating a particular concretized artifact). A explicit commitment to this more abstracted level of representation is a core feature of the SEPIO model, and has implications for how instances in the data are described, identified, and distinguished in practice. In the case that the information artifact is an assertion, the responsible agent is the one who originally generated an assertion based on their evaluation of relevant evidence. If more than one agent is involved in this process, we may consider them collectively as a group or organization representing a single agent. authored_by A relation describing the degree of support provided by an evidence line for a target assertion or proposition. The value of this property is typically a term from some defined set of values that enumerates categorical degrees of evidence strength (e.g. the CIViC five-teired 'evidence level' scale). Different systems or applications can create terms representing the levels of strength they wish to define for their use case. evidence_line_strength A relation indicating whether an evidence line supports or disputes a target proposition (or represents inconclusive evidence that is not sufficient for either). evidenceDirection evidence_direction evidenceItemFor evidence_item_for As an example, consider the assertion that "Variant X causes Disease Y". At an abstract level this represents a bfo: information content entity (or frbr:Work). This abstract assertion can be concretized / encoded various formats - e.g. a free-text sentence, an rdf graph, a blob of json, or stanza of XML. Each such manifestation might use a different model or structure to represent this knowledge. Each such concrete form is considered a separate resource/digital artifact at the 'manifestation' level, but each expresses the same knowledge. The authored_by and date_authored properties allow us connect an abstract or concrete representation of this assertion to who and when the knowledge was originally generated. This will be the same agent and date for all formats/manifestations listed above. The created_by and date_created properties allow us to connect a representation of the abstract or concrete assertion to who and when the specific manifestation was created in a particular format. The agent/dates here will be different for each of the formats/manifestations listed above. A relation between a particular information resource / digital artifact and an agent who made a primary contribution to its original creation. With respect to information resources, this property is used to capture a creator of a particular representation/manifestation of the information content - e.g. as a web resource or digital artifact. To describe the creator of the information content carried by such a digital artifact or resource, us the 'authored_by' property. created_by A relation holding between a plan specification and a planned process it specifies, or the artifact the process generates. specified_creation_of Ontology for Scientific Evidence and Provenance Information The SEPIO ontology is in its early stages of development, undergoing iterative refinement as new requirements emerge and alignment with existing standards is explored. 2023-06-13 An account of a resource. description A related resource from which the described resource is derived. The described resource may be derived from the related resource in whole or in part. Recommended best practice is to identify the related resource by means of a string conforming to a formal identification system. source title true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts true GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' involved in BP If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).