{ "graphs" : [ { "id" : "http://purl.obolibrary.org/obo/t4fs.json", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", "val" : "terms4FAIRskills describes the competencies, skills and knowledge associated with making and keeping data FAIR.\\nThis terminology applies to a variety of use cases, including: assisting with the creation and assessment of stewardship curricula; facilitating the annotation, discovery and evaluation of FAIR-enabling materials \\(e.g. training\\) and resources; enabling the formalisation of job descriptions and CVs with recognised, structured competencies.\\nIt is intended to be of use to trainers who teach FAIR data skills, researchers who wish to identify skill gaps in their teams and managers who need to recruit individuals to relevant roles." }, { "pred" : "http://purl.org/dc/terms/license", "val" : "http://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://purl.org/dc/terms/title", "val" : "terms4FAIRskills (T4FS)" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "terms4FAIRskills by the terms4FAIRskills developers is licensed under CC BY 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", "val" : "2023-03-02" } ], "version" : "http://purl.obolibrary.org/obo/t4fs/releases/2023-03-02/t4fs.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", "lbl" : "example to be eventually removed", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "example to be eventually removed" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000078", "lbl" : "curation status specification", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "curation status specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Bill Bug" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000266" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000103", "lbl" : "failed exploratory term", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "failed exploratory term" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000225", "lbl" : "obsolescence reason specification", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "obsolescence reason specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000120", "lbl" : "metadata complete", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "metadata complete" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000121", "lbl" : "organizational term", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "organizational term" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000122", "lbl" : "ready for release", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "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.\"" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ready for release" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000123", "lbl" : "metadata incomplete", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "metadata incomplete" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000124", "lbl" : "uncurated", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "uncurated" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", "lbl" : "pending final vetting", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "pending final vetting" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000226", "lbl" : "placeholder removed", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "placeholder removed" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000227", "lbl" : "terms merged", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "terms merged" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An editor note should explain what were the merged terms and the reason for the merge." } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000228", "lbl" : "term imported", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "term imported" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000229", "lbl" : "term split", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "term split" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000410", "lbl" : "universal", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "universal" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000409", "lbl" : "denotator type", "type" : "CLASS", "meta" : { "definition" : { "val" : "A denotator type indicates how a term should be interpreted from an ontological perspective." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "denotator type" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Barry Smith, Werner Ceusters" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000420", "lbl" : "defined class", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "defined class" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "\"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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000421", "lbl" : "named class expression", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "named class expression" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000423", "lbl" : "to be replaced with external ontology term", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Terms with this status should eventually replaced with a term from another ontology." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "to be replaced with external ontology term" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000428", "lbl" : "requires discussion", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "requires discussion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMO_0001000", "lbl" : "out of scope", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "http://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", "val" : "https://orcid.org/0000-0001-5208-3432" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000001", "lbl" : "entity", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "entity" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Julius Caesar" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Verdi’s Requiem" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the Second World War" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "your body mass index" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", "lbl" : "continuant", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "continuant" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Continuant" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000003", "lbl" : "occurrent", "type" : "CLASS", "meta" : { "definition" : { "val" : "An entity that has temporal parts and that happens, unfolds or develops through time." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "occurrent" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Occurrent" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000004", "lbl" : "independent continuant", "type" : "CLASS", "meta" : { "definition" : { "val" : "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])" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "ic" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "IndependentContinuant" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a chair" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a heart" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a leg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a molecule" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a spatial region" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an atom" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an orchestra." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an organism" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the bottom right portion of a human torso" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the interior of your mouth" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000015", "lbl" : "process", "type" : "CLASS", "meta" : { "definition" : { "val" : "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])" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "process" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Process" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a process of cell-division, \\ a beating of the heart" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a process of meiosis" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a process of sleeping" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the course of a disease" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the flight of a bird" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the life of an organism" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "your process of aging." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000016", "lbl" : "disposition", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "disposition" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Disposition" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an atom of element X has the disposition to decay to an atom of element Y" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "certain people have a predisposition to colon cancer" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "children are innately disposed to categorize objects in certain ways." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000017", "lbl" : "realizable entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "realizable" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "RealizableEntity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the disposition of this piece of metal to conduct electricity." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the disposition of your blood to coagulate" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the function of your reproductive organs" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of being a doctor" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of this boundary to delineate where Utah and Colorado meet" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000019", "lbl" : "quality", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "quality" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Quality" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the ambient temperature of this portion of air" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the color of a tomato" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the length of the circumference of your waist" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the mass of this piece of gold." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the shape of your nose" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the shape of your nostril" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000020", "lbl" : "specifically dependent continuant", "type" : "CLASS", "meta" : { "definition" : { "val" : "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])" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "sdc" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "SpecificallyDependentContinuant" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "of one-sided specifically dependent continuants: the mass of this tomato" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the disposition of this fish to decay" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the function of this heart: to pump blood" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the mutual dependence of proton donors and acceptors in chemical reactions [79" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the pink color of a medium rare piece of grilled filet mignon at its center" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of being a doctor" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the shape of this hole." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the smell of this portion of mozzarella" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000023", "lbl" : "role", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "role" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Role" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the priest role" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of a boundary to demarcate two neighboring administrative territories" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of a building in serving as a military target" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of a stone in marking a property boundary" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of subject in a clinical trial" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the student role" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7702-4495" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000031", "lbl" : "generically dependent continuant", "type" : "CLASS", "meta" : { "definition" : { "val" : "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])" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "gdc" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "GenericallyDependentContinuant" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000034", "lbl" : "function", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "function" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Function" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the function of a hammer to drive in nails" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the function of a heart pacemaker to regulate the beating of a heart through electricity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the function of amylase in saliva to break down starch into sugar" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000027", "lbl" : "data item", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "data item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Data items include counts of things, analyte concentrations, and statistical summaries." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jonathan Rees" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "data" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000030", "lbl" : "information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A generically dependent continuant that is about some thing." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "information content entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Examples of information content entites include journal articles, data, graphical layouts, and graphs." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000142" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000102", "lbl" : "data about an ontology part", "type" : "CLASS", "meta" : { "definition" : { "val" : "Data about an ontology part is a data item about a part of an ontology, for example a term" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "data about an ontology part" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", "lbl" : "definition", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, "comments" : [ "Allyson Lister 8.10.2019: Although the IAO definition has been included here, we have made a curation decision to allow non-Aristotelian definitions." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "definition" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2012-04-05: \nBarry Smith\n\nThe 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.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour 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. \n\nOn the specifics of the proposed definition:\n\nWe 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. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe 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. " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7702-4495" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000117", "lbl" : "term editor", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "term editor" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "Peter McQuilton" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7702-4495" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000118", "lbl" : "alternative term", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)" }, "comments" : [ "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)." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "alternative label" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "OBO Operations committee" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000119", "lbl" : "definition source", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "definition source" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "Peter McQuilton" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7702-4495" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000136", "lbl" : "is about", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A (currently) primitive relation that relates an information artifact to an entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "This document is about information artifacts and their representations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000233", "lbl" : "term tracker item", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An IRI or similar locator for a request or discussion of an ontology term." }, "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "term tracker item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000052", "lbl" : "characteristic of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "comments" : [ "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." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "inheres in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this fragility is a characteristic of this vase" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this red color is a characteristic of this apple" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "inheres_in" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000053", "lbl" : "has characteristic", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Inverse of characteristic_of" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "bearer of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this apple is bearer of this red color" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this vase is bearer of this fragility" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "bearer_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is bearer of" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000079", "lbl" : "function of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" }, "comments" : [ "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." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this catalysis function is a function of this enzyme" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "function_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is function of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000080", "lbl" : "quality of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" }, "comments" : [ "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." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this red color is a quality of this apple" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "A quality inheres in its bearer at all times for which the quality exists." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is quality of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "quality_of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000081", "lbl" : "role of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" }, "comments" : [ "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." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this investigator role is a role of this person" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is role of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "role_of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000085", "lbl" : "has function", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_function" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000086", "lbl" : "has quality", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this apple has quality this red color" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_quality" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000087", "lbl" : "has role", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_role" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000091", "lbl" : "has disposition", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000092", "lbl" : "disposition of", "type" : "PROPERTY", "meta" : { "comments" : [ "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." ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000002", "lbl" : "pipe separated values", "type" : "CLASS", "meta" : { "definition" : { "val" : "A file that contains the values in a table as a series of ASCII text lines organized so that each column value is separated by a pipe." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7702-4495" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000004", "lbl" : "software preservation", "type" : "CLASS", "meta" : { "definition" : { "val" : "Software preservation involves the collection and long-term storage of software for archiving as well as maintaining availability and accessibility." }, "comments" : [ "AL 8.2.22: Refactored \"software review and preservation\" to \"software preservation\", as the review process is not within the remit of terms4FAIRskills. Added definition and source." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Kristina Hettne" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Victoria Dominguez Del Angel" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Yann Le Franc" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7702-4495" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000005", "lbl" : "repository access", "type" : "CLASS", "meta" : { "definition" : { "val" : "In accessing a repository one uses a client (application) to discover relevant digital objects within a repository, and then retrieve a copy of a desired digital object." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7702-4495" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000006", "lbl" : "develop fair and open research vision", "type" : "CLASS", "meta" : { "definition" : { "val" : "Include FAIR and open research in the strategic framework for the organization and set objectives and timeframe." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Angus Whyte" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Celia van Gelder" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mateusz Kuzak" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Yan Wang" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000008", "lbl" : "develop open research strategy and vision", "type" : "CLASS", "meta" : { "definition" : { "val" : "The activity of developing an open research strategy and vision." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Angus Whyte" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Celia van Gelder" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mateusz Kuzak" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Yan Wang" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000009", "lbl" : "data management policy", "type" : "CLASS", "meta" : { "definition" : { "val" : "A written document backed by management describing policy and providing guidance to ensure that appropriate standards, consistent guidelines, and common strategies are used, providing linkages to and consistency with other similar systems, and fostering a true network across an organization producing data." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000010", "lbl" : "understand research code of conduct", "type" : "CLASS", "meta" : { "definition" : { "val" : "Understand how the governing principles of research integrity and FAIR overlap" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Angus Whyte" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Celia van Gelder" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000011", "lbl" : "choosing the appropriate reporting guideline for your data", "type" : "CLASS", "meta" : { "definition" : { "val" : "To be able to choose the appropriate reporting guideline/checklist for your data, based on community-adopted standards." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000012", "lbl" : "data stewardship activity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A specific deed, action, function or sphere of action in relation with the role of data stewardship" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Yann Le Franc" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7702-4495" }, { "pred" : "http://purl.obolibrary.org/obo/T4FS_0000564", "val" : "Set of actions carried out during data stewardship processes" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000013", "lbl" : "data munging", "type" : "CLASS", "meta" : { "definition" : { "val" : "A series of potentially destructive or irrevocable changes to a piece of data or a file. 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Registration must be accompanied by the step(s) to upload the data object to a persistent repository." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7702-4495" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000020", "lbl" : "interoperability", "type" : "CLASS", "meta" : { "definition" : { "val" : "The capability to communicate, execute programs, or transfer data among various functional units in a useful and meaningful manner that requires the user to have little or no knowledge of the unique characteristics of those units. Foundational, syntactic, and semantic interoperability are the three necessary aspects of interoperability." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000021", "lbl" : "exposing data", "type" : "CLASS", "meta" : { "definition" : { "val" : "Exposing data is the activity of exposing your data to collaborators, the public, or other interested parties. A data producer makes the data accessible to external users in a machine- and/or human-readable way." }, "comments" : [ "AL 15.3.22: Was \"expose your data\", which was not in the style of other term labels. Also updated definition, but might need revisiting later for a more formal definition." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7702-4495" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000023", "lbl" : "aptitudes for workflow technologies management", "type" : "CLASS", "meta" : { "definition" : { "val" : "Bin for Aptitudes related to Workflow technologies management." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "leightonlc" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000024", "lbl" : "de facto standard", "type" : "CLASS", "meta" : { "definition" : { "val" : "A standard that is widely accepted and used, but lacks formal approval by a recognized standards developing organization (e.g., the QWERTY keyboard)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000025", "lbl" : "data entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "An object, event, or phenomenon about which data are stored in a database and which has intermediate representation in a Data Model." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000026", "lbl" : "real-time data", "type" : "CLASS", "meta" : { "definition" : { "val" : "Data that are being received, processed and stored at the time of their occurrence with only small delays. Examples include: stock quotes, manufacturing statistics, Web server loads, data warehouse activity and sensor feeds to data collectors. Real-time data are data streams that are typically generated by sensors and received via direct networking connections." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7702-4495" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000027", "lbl" : "storage security risk assessment and mitigation", "type" : "CLASS", "meta" : { "definition" : { "val" : "Detect and analysis security risk of storage periodically, and minimize the impact of the risks detected" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Angus Whyte" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Celia van Gelder" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mateusz Kuzak" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Yan Wang" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000028", "lbl" : "remote access", "type" : "CLASS", "meta" : { "definition" : { "val" : "The ability to get access to a computer or a network from a remote distance. Access may be through an Internet service provider (ISP) or through a dedicated line between a computer or a remote local area network and the central or main corporate local area network. A dedicated line is more expensive and less flexible but offers faster data rates." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7702-4495" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000029", "lbl" : "fair stewardship supervising", "type" : "CLASS", "meta" : { "definition" : { "val" : "The activity of supervision of other people to ensure FAIR data practices." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Philippe Rocca-Serra" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Susanna Sansone" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7702-4495" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000030", "lbl" : "skills related to high performance computing management", "type" : "CLASS", "meta" : { "definition" : { "val" : "Bin for Skills needed for High performance computing management." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "leightonlc" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000031", "lbl" : "fair metrics selection skills", "type" : "CLASS", "meta" : { "definition" : { "val" : "Ability to select the appropriate FAIR metrics among the existing ones in relation to the type of digital object concerned." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Kristina Hettne" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Victoria Dominguez Del Angel" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Yann Le Franc" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000032", "lbl" : "relational database", "type" : "CLASS", "meta" : { "definition" : { "val" : "A collection of data items organized as a set of formally-described tables from which data can be accessed or reassembled in many different ways without having to reorganize the database tables. 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Note that a version is different from a backup copy, which is typically a copy made at a specific point in time, or a replica." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7702-4495" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000041", "lbl" : "understanding fair and open research challenges in your organization", "type" : "CLASS", "meta" : { "definition" : { "val" : "Understand the FAIR and open research practices, and the research landscape / current data management practices in the organization." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Angus Whyte" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Celia van Gelder" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mateusz Kuzak" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Yan Wang" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000042", "lbl" : "ethical application of patents, licenses", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000043", "lbl" : "data access protocol", "type" : "CLASS", "meta" : { "definition" : { "val" : "A system that allows outsiders to be granted access to databases without overloading the system." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000044", "lbl" : "data processing", "type" : "CLASS", "meta" : { "definition" : { "val" : "A generic concept referring to all kinds of procedures being executed on data at any point in the data life cycle." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000045", "lbl" : "data organization", "type" : "CLASS", "meta" : { "definition" : { "val" : "Denotes the complexity of measures that are used by a repository to form aggregations of data objects (including collections and metadata) to describe the properties of data objects, to register PIDs, to build the PID records, to link between all components, and to set up the containers (software stack) that are used to store all..." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000046", "lbl" : "data rescue", "type" : "CLASS", "meta" : { "definition" : { "val" : "Recovery and/or transformation and digitization of dark data and at-risk data so that they can be preserved, accessed, shared, and used. Data rescue also involves the addition of rich metadata to make the content understandable and more easily re-usable." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7702-4495" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000047", "lbl" : "understand societal impact of research", "type" : "CLASS", "meta" : { "definition" : { "val" : "Anticipate possible implications of the research and making its outputs FAIR, reflecting on rmotivations and areas of uncertainty" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Angus Whyte" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Celia van Gelder" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mateusz Kuzak" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Yan Wang" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000048", "lbl" : "searching via algorithms and software", "type" : "CLASS", "meta" : { "definition" : { "val" : "To be able to search using software with a GUI or terminal access. For example using BLAST or genomic search tools in the life sciences." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "Algorithm searching" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "Programmatic search" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "batch search" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000049", "lbl" : "audit", "type" : "CLASS", "meta" : { "definition" : { "val" : "An independent evaluation of an organization, system, process, project or product." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Peter McQuilton" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000050", "lbl" : "wiki site", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "Peter McQuilton" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-10-01T21:03:37.147424Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000051", "lbl" : "skills related to authorisation management", "type" : "CLASS", "meta" : { "definition" : { "val" : "Bin for Skills needed for Authorization management." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "leightonlc" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000053", "lbl" : "storage management", "type" : "CLASS", "meta" : { "definition" : { "val" : "The term storage management encompasses the technologies and processes organizations use to maximize or improve the performance of their data storage resources. It is a broad category that includes virtualization, replication, mirroring, security, compression, traffic analysis, process automation, storage provisioning and related techniques." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Kristina Hettne" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Simon Hodson" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Victoria Dominguez Del Angel" } ] } }, { "id" : "http://purl.obolibrary.org/obo/T4FS_0000054", "lbl" : "data warehouse", "type" : "CLASS", "meta" : { "definition" : { "val" : "A central repository for all or significant parts of the data that an organization's various business systems collect. A data warehouse tends to be a strategic but somewhat unfinished concept. Data warehousing emphasizes the capture of data from diverse sources for useful analysis and access, but does not generally start from the point-of-view of the …