Contributor Role Ontology Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label 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 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 OBI_0000281 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.obfoundry.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 term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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 curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester ontology term requester 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 elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg term replaced by term replaced by temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime 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 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 http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See 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 inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer of 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 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 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]) 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] specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] 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] CRO:0000000 contributor role http://purl.obolibrary.org/obo/IAO_0000120 A high-level classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. https://orcid.org/0000-0001-5059-4132 http://dictionary.casrai.org/Contributor_Roles 9dbb95f4-55ed-4e43-9301-a9f0e3e17afe contributor role CRO:0000001 Creation and/or presentation of a published research object, such as books, journal articles, and other publications like technical documentation, web sites, code, ontologies, or data models. writer role 2018-09-14T19:47:01Z author role Creation and/or presentation of a published research object, such as books, journal articles, and other publications like technical documentation, web sites, code, ontologies, or data models. https://orcid.org/0000-0002-1048-5019 CRO:0000003 Preparation, creation and/or presentation of figures for a manuscript, presentation or other use. 2018-09-14T19:49:22Z figure development role Preparation, creation and/or presentation of figures for a manuscript, presentation or other use. http://dictionary.casrai.org/Contributor_Roles/Visualization CRO:0000004 Translating words or text from one language to another. 2018-09-14T19:49:51Z translator role CRO:0000006 Includes literature searches and contributions to review activities (systematic reviews, scoping reviews, etc.) 2018-09-14T19:51:01Z background and literature search role CRO:0000007 Coordination of research dissemination through popular media and the press, as well as community outreach and liaising of project directly to the community. Similar to vivo:OutreachProviderRole? communication role outreach role 2018-09-14T19:51:26Z marketing and communication role CRO:0000008 Creation or refinement of a website, a set of related web pages served from a single web domain. website development role website maintenance role 2018-09-14T19:51:53Z website role Creation or refinement of a website, a set of related web pages served from a single web domain. https://www.wikidata.org/wiki/Q35127 CRO:0000009 A communication role that encompasses facilitate co-operation between people or organizations. 2018-09-14T19:52:02Z obsolete networking facilitation role true A communication role that encompasses facilitate co-operation between people or organizations. (2009) The functions and roles of network facilitators. In: Franz HW., Sarcina R. (eds) Building Leadership in Project and Network Management. Springer, Berlin, Heidelberg CRO:0000010 A communication role that involves the activity, set of institutions, and processes for creating, communicating, delivering, and exchanging offerings that have value for customers, clients, partners, and society at large. 2018-09-14T19:52:12Z obsolete marketing role true A communication role that involves the activity, set of institutions, and processes for creating, communicating, delivering, and exchanging offerings that have value for customers, clients, partners, and society at large. https://www.ama.org/the-definition-of-marketing/ CRO:0000011 A communication role in which one records the details of an event, a process, a workflow, etc. 2018-09-14T19:52:17Z documentation role A communication role in which one records the details of an event, a process, a workflow, etc. https://dictionary.cambridge.org/us/dictionary/english/document CRO:0000012 A communication role that utilizes the art or profession of using design elements (such as typography and images) to convey information, create visualizations, or create an effect. 2018-09-14T19:52:27Z graphic design role A communication role that utilizes the art or profession of using design elements (such as typography and images) to convey information, create visualizations, or create an effect. https://www.merriam-webster.com/dictionary/graphic%20design CRO:0000014 Creation of software documentation. software documentation role 2018-09-14T20:26:05Z technical documentation role CRO:0000015 A role that encompasses effective and efficient operation and usage of data, including, but not limited to management, handling, or manipulation. 2018-09-14T19:55:34Z data role CRO:0000016 A role in which a person participates in the transfer of knowledge and skills, through teaching, development of educational materials or curriculum, through program development or other means. educational role 2018-09-14T19:55:45Z education and training role CRO:0000018 A role that involves the development, management, and use of computer-based information systems. 2018-09-14T19:56:05Z obsolete information technology systems role true A role that involves the development, management, and use of computer-based information systems. https://www.wikidata.org/wiki/Q11661 CRO:0000019 Verification that software meets requirements; validation that software meets users' needs, identification of software bugs, assessment of software performance and usability. Software Quality Assurance Role 2018-09-14T20:26:00Z software testing role CRO:0000020 A role related to creations of the mind, such as inventions; literary and artistic works; designs; and symbols, names and images used in commerce. from. 2018-09-14T19:56:34Z intellectual property role A role related to creations of the mind, such as inventions; literary and artistic works; designs; and symbols, names and images used in commerce. from. https://www.wipo.int/about-ip/en/ CRO:0000022 Policy development generally involves research, analysis, consultation and synthesis of information to produce recommendations for action by an individual or an organization. It should also involve an evaluation of options against a set of criteria used to assess each option. 2018-09-14T20:04:29Z policy development role CRO:0000023 Set of activities aimed at prolonging the life of a record. 2018-09-14T20:04:39Z preservation role Set of activities aimed at prolonging the life of a record. https://www.wikidata.org/wiki/Q830393 CRO:0000025 Manage regulatory and compliance issues for the research project. regulatory administration role 2018-09-14T20:05:56Z regulatory and compliance role CRO:0000026 A person that is responsible for usage of instrumentation, such as equipment or devices, or instruments like a survey or questionnaire. 2018-09-14T20:06:00Z instrumentation role CRO:0000027 Management activities to annotate, maintain, research, and preserve physical objects to maximize their use for research and education now and into the future. https://orcid.org/0000-0002-2908-3327 curator role CRO:0000028 Activities to obtain physical objects for research or scholarly purposes or to add to a collection. https://orcid.org/0000-0002-2908-3327 collection role CRO:0000031 Coordination of diverse team members, often across different disciplines and locations. 2018-09-14T20:06:26Z team management role CRO:0000033 The compiling of information with intent to prepare combined datasets for data processing. 2018-09-14T20:11:23Z obsolete data aggregation role true The compiling of information with intent to prepare combined datasets for data processing. Stanley, Jay; Steinhardt, Barry (January 2003). "Bigger Monster, Weaker Chains: The Growth of an American Surveillance Society". American Civil Liberties Union. CRO:0000035 Statistical aspects of research, including data collection, organization, analysis, interpretation and presentation of data from surveys and experiments statistical data analysis role 2018-09-14T20:11:35Z statistical analysis role Statistical aspects of research, including data collection, organization, analysis, interpretation and presentation of data from surveys and experiments https://en.wikipedia.org/wiki/Statistics CRO:0000036 The process of gathering and measuring data, information or any variables of interest in a standardized and established manner that enables the collector to answer or test hypothesis and evaluate outcomes of the particular collection. data aggregation role 2018-09-14T20:11:40Z data collection role The process of gathering and measuring data, information or any variables of interest in a standardized and established manner that enables the collector to answer or test hypothesis and evaluate outcomes of the particular collection. https://www.techopedia.com/definition/30318/data-collection CRO:0000038 The annotation of data with descriptive information that describes the data (metadata), with the goal of making the data more usuable or reusable for future use. metadata application role 2018-09-14T20:11:50Z metadata role The annotation of data with descriptive information that describes the data (metadata), with the goal of making the data more usuable or reusable for future use. https://whatis.techtarget.com/definition/metadata-management CRO:0000039 The process of inputting data into a computerized form. 2018-09-14T20:11:54Z data entry role The process of inputting data into a computerized form. https://www.dictionary.com/browse/data-entry CRO:0000040 The process of combining data from different sources to provide a standardized or unified view. 2018-09-14T20:12:00Z data integration role The process of combining data from different sources to provide a standardized or unified view. https://www.wikidata.org/wiki/Q386824 CRO:0000041 The process of creating a data model for an information system by applying certain formal techniques. 2018-09-14T20:12:07Z data modeling role The process of creating a data model for an information system by applying certain formal techniques. https://www.wikidata.org/wiki/Q367664 CRO:0000042 A procedure intended to verify the efficiency and reliability of data. Data Scrubbing Role 2018-09-14T20:12:14Z data quality assurance role A procedure intended to verify the efficiency and reliability of data. https://www.techopedia.com/definition/14653/data-quality CRO:0000043 The process of creating data standards, which are the rules by which data are described and recorded in order to share, exchange, and understand data. Examples include development of an ontology, terminology, code lists, etc. 2018-09-14T20:12:25Z obsolete data standards developer role true The process of creating data standards, which are the rules by which data are described and recorded in order to share, exchange, and understand data. Examples include development of an ontology, terminology, code lists, etc. https://www.usgs.gov/products/data-and-tools/data-management/data-standards CRO:0000045 An educational role in which a person develops educational or training materials that are intended to transfer knowledge, for use in a classroom, indpendent learning or other settings. educational material development role 2018-09-14T20:15:18Z training material role CRO:0000046 An educational role in which a person participates in the development of an educational program, designed for learners to achieve a set of compentencies around a given topic or area of focus. educational program development role 2018-09-14T20:15:23Z training program development role CRO:0000047 An educational role in which knowledge and skills are transferred through teaching. This may be equivalent to vivo:Teacher Role. educational instruction role educational training role teaching role 2018-09-14T20:15:29Z instruction role An educational role in which knowledge and skills are transferred through teaching. https://www.wikidata.org/wiki/Q8434 CRO:0000048 An information technology systems role that specifically focuses on the computer hardware, the physical components of a computer system. hardware systems role 2018-09-14T20:17:16Z hardware role An information technology systems role that specifically focuses on the computer hardware, the physical components of a computer system. https://www.wikidata.org/wiki/Q3966 CRO:0000049 An information technology systems role that specifically focuses on the computer software, the non-tangible executable component of a computer. 2018-09-14T20:17:20Z obsolete software systems role true An information technology systems role that specifically focuses on the computer software, the non-tangible executable component of a computer. https://www.wikidata.org/wiki/Q7397 CRO:0000050 A role usually within the Information Technology department, charged with the creation, maintenance, backups, querying, tuning, user rights assignment and security of an organization's databases. database administration role 2018-09-14T20:17:25Z database administrator role A role usually within the Information Technology department, charged with the creation, maintenance, backups, querying, tuning, user rights assignment and security of an organization's databases. https://www.techopedia.com/definition/1187/database-administrator-dba CRO:0000051 A software systems role that involves maintenance and operation of a computer system and/or network. sysadmin role systems administration role 2018-09-14T20:17:32Z system administrator role A software systems role that involves maintenance and operation of a computer system and/or network. https://www.wikidata.org/wiki/Q327353 CRO:0000052 A methodology role that involves development of information that suggests how something should be done. Best Practices Role guideline development role standard operating procedure development role 2018-09-14T20:19:52Z standards role A methodology role that involves development of information that suggests how something should be done. https://dictionary.cambridge.org/us/dictionary/english/guideline CRO:0000053 A methodology role that involves creation of a detailed plan of a scientific or medical experiment, treatment, or procedure. protocol development role 2018-09-14T20:19:56Z protocol creation role A methodology role that involves creation of a detailed plan of a scientific or medical experiment, treatment, or procedure. https://www.merriam-webster.com/dictionary/protocol CRO:0000054 A methodology role that involves the development or creation of an established or prescribed methods to be followed routinely for the performance of designated operations or in designated situations. 2018-09-14T20:20:02Z obsolete standard operating procedure development role true A methodology role that involves the development or creation of an established or prescribed methods to be followed routinely for the performance of designated operations or in designated situations. https://www.merriam-webster.com/dictionary/standard%20operating%20procedure CRO:0000055 Detailed design of study components including data collection, analysis, and dissemination. 2018-09-14T20:20:06Z study design role CRO:0000056 A methodology role that involves the creation or refinement of a manner or method by which an activity is performed. 2018-09-14T20:20:11Z technique development role A methodology role that involves the creation or refinement of a manner or method by which an activity is performed. https://www.wikidata.org/wiki/Q2695280 CRO:0000057 A role charged with conceptualization, design, development and marketing of complex equipment. instrument development role 2018-09-14T20:23:39Z device development role A role charged with conceptualization, design, development and marketing of complex equipment. https://searchcio.techtarget.com/definition/product-development-or-new-product-development-NPD CRO:0000058 A person that is responsible for operating equipment or instrumentation and/or that ensures equipment is well-maintained, properly configured, and safely functional. instrument technician role 2018-09-14T20:23:44Z equipment technician role A person that is responsible for operating equipment or instrumentation and/or that ensures equipment is well-maintained, properly configured, and safely functional. https://en.wikipedia.org/wiki/Biomedical_equipment_technician CRO:0000059 Creation or refinement of a survey or questionnaire, a list of questions aimed at extracting specific data from a particular group of people. 2018-09-14T20:23:49Z survey and questionnaire development role Creation or refinement of a survey or questionnaire, a list of questions aimed at extracting specific data from a particular group of people. https://www.wikidata.org/wiki/Q7257997 CRO:0000060 Examination of software code to identify build-breaking changes prior to acceptance into a codebase. software code review role 2018-09-14T20:25:30Z code review role CRO:0000061 Algorithm development and implementation of software in a computer programming language. 2018-09-14T20:25:35Z obsolete computer programming role true CRO:0000062 Creation of high-level structures of a software system. 2018-09-14T20:25:40Z software architecture role CRO:0000063 Creation of low-level software component and algorithm design. 2018-09-14T20:25:45Z software design role Creation of low-level software component and algorithm design. https://en.wikipedia.org/wiki/Low-level_design CRO:0000064 Systematic application of scientific and technological knowledge, methods, and experience to the design, implementation, testing, and documentation of software. computer programming role 2018-09-14T20:25:49Z software engineering role CRO:0000065 Planning, management, and monitoring of projects. 2018-09-14T20:25:55Z project management role CRO:0000067 A professional who assesses, collects, organizes, preserves, maintains control over, and provides access to information determined to have long-term value. 2018-09-15T16:25:54Z archivist role A professional who assesses, collects, organizes, preserves, maintains control over, and provides access to information determined to have long-term value. https://www.wikidata.org/wiki/Q635734 CRO:0000068 A person responsible for the preservation of artistic and cultural artifacts. 2018-09-15T16:26:00Z conservator role A person responsible for the preservation of artistic and cultural artifacts. https://www.wikidata.org/wiki/Q446966 CRO:0000069 A role that includes the formal endeavor to ensure that digital information of continuing value remains accessible, trustworthy, and usable. 2018-09-15T16:26:05Z digital preservation role A role that includes the formal endeavor to ensure that digital information of continuing value remains accessible, trustworthy, and usable. https://www.wikidata.org/wiki/Q632897 CRO:0000070 2018-09-15T16:29:29Z relationship CRO:0000071 2018-09-15T16:29:43Z contributorship CRO:0000072 Aggregation, integration, manipulation of data. data manipulation role 2018-10-01T20:32:37Z data transformation role CRO:0000073 The process of creating standards, which aare an established norm or requirement in regard to technical systems. It is usually a formal document that establishes uniform engineering or technical criteria, methods, processes, and practices. standard development role 2018-10-01T20:33:58Z standards development role The process of creating standards, which aare an established norm or requirement in regard to technical systems. It is usually a formal document that establishes uniform engineering or technical criteria, methods, processes, and practices. https://en.wikipedia.org/wiki/Technical_standard CRO:0000074 Verification, whether as a part of the activity or separate, of the overall replication/reproducibility of results/experiments and other research outputs. 2018-10-01T20:35:43Z data validation role CRO:0000075 formal training role 2018-10-01T20:42:52Z educational training role true CRO:0000076 A role that includes the design and implementation of the physical components of a computer system. information technology hardware systems design and implementation role 2018-10-01T20:43:37Z obsolete IT hardware systems design and implementation role true A role that includes the design and implementation of the physical components of a computer system. https://www.wikidata.org/wiki/Q3966 CRO:0000077 2018-10-01T20:44:21Z systems administration role true CRO:0000078 Contribution to the basic, underlying framework or features of a system or organization. 2018-10-01T20:48:11Z infrastructure role Contribution to the basic, underlying framework or features of a system or organization. https://www.dictionary.com/browse/infrastructure CRO:0000079 Evaluation is a systematic method for collecting, analyzing, and using information to answer questions about projects, policies and programs, particularly about their effectiveness and efficiency. 2018-10-01T20:48:24Z project, policy or program evaluation role Evaluation is a systematic method for collecting, analyzing, and using information to answer questions about projects, policies and programs, particularly about their effectiveness and efficiency. https://en.wikipedia.org/wiki/Program_evaluation CRO:0000080 An infrastructure role that is accountable for management and coordination of a program, to help achieve the program goals. 2018-10-01T20:48:37Z obsolete program administration role true CRO:0000081 The organization of the different elements needed to implement a study. 2018-10-01T20:49:10Z coordination role The organization of the different elements needed to implement a study. https://learn.nursing.jhu.edu/face-to-face/courses/research-coordinator/index.html CRO:0000082 Oversight and leadership responsibility for the research activity planning and execution, including mentorship external to the core team. 2018-10-01T20:49:54Z supervisory role true CRO:0000083 A communication role which involves the dynamic relational process that facilitates communication, interaction, involvement, and exchange between an organization and a community for a range of social and organizational outcomes. 2018-10-01T20:55:22Z community engagement role A communication role which involves the dynamic relational process that facilitates communication, interaction, involvement, and exchange between an organization and a community for a range of social and organizational outcomes. Johnston, K. A. (2018). Toward a theory of social engagement. In K. A. Johnston & M. Taylor (Eds.), The Handbook of Communication Engagement (pp. 19-32). Hoboken, NJ: Wiley. CRO:0000084 A communication role that involves development or production of materials, such as brochures, websites, flyers, presentations, etc., for the purposes of promotion of a entity, like a project, group or organization. 2018-10-01T20:56:18Z outreach materials development role CRO:0000085 Role that involves identifying eligible participants, explaining the study to potential participants, recruiting an adequate sample based on study goals and design, obtaining informed consent/maintaining ethical standards, and retaining participants until study completion. 2018-10-01T20:57:17Z obsolete participant recruitment role true Role that involves identifying eligible participants, explaining the study to potential participants, recruiting an adequate sample based on study goals and design, obtaining informed consent/maintaining ethical standards, and retaining participants until study completion. https://healthit.ahrq.gov/ahrq-funded-projects/emerging-lessons/participant-recruitment-research CRO:0000086 Ideas; formulation or evolution of overarching research goals and aims. 2018-10-01T20:57:53Z research conceptualization role true CRO:0000087 One who is proficient in the relevant skill and technique, with a relatively practical understanding of the theoretical principles. 2018-10-01T20:58:59Z technician role One who is proficient in the relevant skill and technique, with a relatively practical understanding of the theoretical principles. https://en.wikipedia.org/wiki/Technician CRO:0000088 Creation and/or presentation of the published work, specifically writing the initial draft (including substantive translation). 2018-10-01T21:03:36Z original draft preparation role true CRO:0000089 A role in which one provides a summary of a research output, such as a journal article, that is understandable by a lay person or non-expert audience. lay synthesis of research output role 2018-10-01T21:04:14Z lay summary role CRO:0000090 A method or steps that maintain, update content, clean up, or repair a website. 2018-10-01T21:13:13Z obsolete website maintenance role true A method or steps that maintain, update content, clean up, or repair a website. https://www.wikidata.org/wiki/Q17634596 CRO:0000091 A documentation role that involves preparation of instruction manuals, journal articles, and other supporting documents to communicate complex and technical information more easily. technical writing role A documentation role that involves preparation of instruction manuals, journal articles, and other supporting documents to communicate complex and technical information more easily. https://www.truity.com/career-profile/technical-writer CRO:0000092 The tasks that go into determining the needs or conditions to meet for a new or altered software product or project, taking account of the possibly conflicting requirements of the various stakeholders, analyzing, documenting, validating and managing software or system requirements. requirements analysis role The tasks that go into determining the needs or conditions to meet for a new or altered software product or project, taking account of the possibly conflicting requirements of the various stakeholders, analyzing, documenting, validating and managing software or system requirements. Kotonya, G. and Sommerville, I. 1998. Requirements Engineering: Processes and Techniques Chichester, UK: John Wiley and Sons. CRO:0000093 Obtaining a material entity for potential use as an input during an investigation. https://orcid.org/0000-0002-2908-3327 specimen collection role CRO:0000094 In botany, this is the collector listed first for a particular specimen. Each specimen has one primary collector. The primary collector assigns a number to that specimen from his/her own number series. http://orcid.org/0000-0002-2908-3327 primary collector role CRO:0000095 Evaluation of grant applications by others working in the same field. https://orcid.org/0000-0001-9114-8737 grant peer review role CRO:0000096 Selecting, ordering, and receiving materials or physical objects for research, scholarly, library or archival collections. https://orcid.org/0000-0002-2908-3327 acquisition role CRO:0000097 The person or organization that provides money for a particular purpose, such as a grant to perform research. funder role funding source role The person or organization that provides money for a particular purpose, such as a grant to perform research. https://www.lexico.com/en/definition/funder CRO:0000098 The person or organization that is responsible for a new or novel discovery, i.e., the process of finding information, a place, or an object, especially for the first time, or the thing that is found. For example, a researcher discovering a new gene mutation that contributes to a disease. discovery role The person or organization that is responsible for a new or novel discovery, i.e., the process of finding information, a place, or an object, especially for the first time, or the thing that is found. For example, a researcher discovering a new gene mutation that contributes to a disease. https://dictionary.cambridge.org/us/dictionary/english/discovery CRO:0000099 A person or organization who helps guide a patient through the healthcare system. This includes help going through the screening, diagnosis, treatment (including clinical trials), and follow-up of a medical condition, such as cancer. patient advocate role A person or organization who helps guide a patient through the healthcare system. This includes help going through the screening, diagnosis, treatment (including clinical trials), and follow-up of a medical condition, such as cancer. https://www.cancer.gov/publications/dictionaries/cancer-terms/def/patient-advocate CRO:0000100 Oral presentation intended to present information or teach people about a particular subject, such as a talk or poster presentation at a conference. lecture role lecturer role presentation role speaker role presenter role Oral presentation intended to present information or teach people about a particular subject, such as a talk or poster presentation at a conference. https://www.wikidata.org/wiki/Q603773 CRO:0000101 Evaluation of scientific, academic, or professional work, such as manuscripts or grants by others working in the same field. manuscript review role peer review role Evaluation of scientific, academic, or professional work, such as manuscripts or grants by others working in the same field. https://www.lexico.com/en/definition/peer_review CRO:0000102 A role that involves giving advice in a particular field. https://orcid.org/0000-0001-8420-5254 advisory role advisory role https://www.lexico.com/en/definition/adviser CRO:0000103 A role that is realized through the modification of an existing artifact (e.g. adding or removing content to/from a document, updating information in a data record, fixing errors in a manuscript, etc.) updater role https://orcid.org/0000-0002-1048-5019 The nature of a modification will vary depending on the type of artifact being modified, and more specific terms may exist in the CRO to describe certain types of modification. modifier role A role that is realized through the modification of an existing artifact (e.g. adding or removing content to/from a document, updating information in a data record, fixing errors in a manuscript, etc.) https://orcid.org/0000-0002-1048-5019 CRO:0000104 A role that is realized through the act of formally accepting an artifact for inclusion in some larger resource (e.g. database, registry, collection, etc.) https://orcid.org/0000-0002-1048-5019 An agent accepting an artifact possesses the authority to decide if it belongs in a particular resource or collection. This agent may or may not also have directly evaluated it themselves - but if they did, an 'evaluator role' could additionally be captured. acceptor role A role that is realized through the act of formally accepting an artifact for inclusion in some larger resource (e.g. database, registry, collection, etc.) https://orcid.org/0000-0002-1048-5019 CRO:0000105 A role that is realized through the act of formally submitting or depositing an artifact to be included in some larger resource (e.g. database, registry, collection, etc.) depositor role https://orcid.org/0000-0002-1048-5019 An agent submitting an artifact may or may not also have contributed to its creation. If they did, and additional ‘creator role’ can be applied. submitter role A role that is realized through the act of formally submitting or depositing an artifact to be included in some larger resource (e.g. database, registry, collection, etc.) https://orcid.org/0000-0002-1048-5019 CRO:0000106 A role that is realized through the review and evaluation of an artifact - generally to assess its quality, completeness, relevance, or other characteristics. assessor role reviewer role https://orcid.org/0000-0002-1048-5019 Evaluating an artifact does not involve modification of the assessed artifact - 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, a 'modifier role' should additionally be applied. evaluator role A role that is realized through the review and evaluation of an artifact - generally to assess its quality, completeness, relevance, or other characteristics. https://orcid.org/0000-0002-1048-5019 CRO:0000107 A role used to indicate that an agent was the creator of an artifact (i.e. had significant or sole responsibility for its initial generation). https://orcid.org/0000-0002-1048-5019 This is a generic role to be used when a more specific term suitable for the contribution scenario is not available or warranted. For example, the 'author role' term describes creator roles for published works, and should be used to describe creation of things like books or journal articles. creator role A role used to indicate that an agent was the creator of an artifact (i.e. had significant or sole responsibility for its initial generation). https://orcid.org/0000-0002-1048-5019 CRO:0000108 A role that involves creation, maintenance or administration of a database. https://orcid.org/0000-0001-8420-5254 database role CRO:0000110 https://orcid.org/0000-0001-8420-5254 community research partner CRO:0000111 A person who deals with provision and maintenance of information in many formats, including: books; electronic resources; magazines; newspapers; audio and video recordings; maps; manuscripts; photographs and other graphic material; bibliographic databases; and web-based and digital resources. A librarian may also provide other information services, including: information literacy instruction; computer provision and training; coordination with community groups to host public programs; assistive technology for people with disabilities; and assistance locating community resources. Librarians often work in a library, but can also work in other physical settings or virtual environments. https://orcid.org/0000-0001-8420-5254 librarian role A person who deals with provision and maintenance of information in many formats, including: books; electronic resources; magazines; newspapers; audio and video recordings; maps; manuscripts; photographs and other graphic material; bibliographic databases; and web-based and digital resources. A librarian may also provide other information services, including: information literacy instruction; computer provision and training; coordination with community groups to host public programs; assistive technology for people with disabilities; and assistance locating community resources. Librarians often work in a library, but can also work in other physical settings or virtual environments. https://en.wikipedia.org/wiki/Librarian 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/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item IAO:0000030 information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 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). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity 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:0000102 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: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:0000409 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 conceptualization role http://purl.obolibrary.org/obo/IAO_0000120 Ideas; formulation or evolution of overarching research goals and aims. https://orcid.org/0000-0001-5059-4132 research conceptualization role http://dictionary.casrai.org/Contributor_Roles/Conceptualization http://purl.org/credit/ontology 8b73531f-db56-4914-9502-4cc4d4d8ed73 conceptualization role data curation role http://purl.obolibrary.org/obo/IAO_0000120 Management activities to annotate (produce metadata), scrub data and maintain research data (including software code, where it is necessary for interpreting the data itself) for initial use and later re-use. https://orcid.org/0000-0001-5059-4132 http://dictionary.casrai.org/Contributor_Roles/Data_curation http://purl.org/credit/ontology f93e0f44-f2a4-4ea1-824a-4e0853b05c9d data curation role formal analysis role http://purl.obolibrary.org/obo/IAO_0000120 Application of statistical, mathematical, computational, or other formal techniques to analyse or synthesize study data. https://orcid.org/0000-0001-5059-4132 data analysis role http://dictionary.casrai.org/Contributor_Roles/Formal_analysis http://purl.org/credit/ontology 95394cbd-4dc8-4735-b589-7e5f9e622b3f formal analysis role funding acquisition role http://purl.obolibrary.org/obo/IAO_0000120 Acquisition of the financial support for the project leading to this publication. https://orcid.org/0000-0001-5059-4132 grant acquisition role http://dictionary.casrai.org/Contributor_Roles/Funding_acquisition http://purl.org/credit/ontology 34ff6d68-132f-4438-a1f4-fba61ccf364 funding acquisition role investigation role http://purl.obolibrary.org/obo/IAO_0000120 Conducting a research and investigation process, specifically performing the experiments, or data/evidence collection. https://orcid.org/0000-0001-5059-4132 http://dictionary.casrai.org/Contributor_Roles/Investigation http://purl.org/credit/ontology 2451924d-425e-4778-9f4c-36c848ca70c2 investigation role methodology role http://purl.obolibrary.org/obo/IAO_0000120 Development or design of methodology; creation of models. https://orcid.org/0000-0001-5059-4132 http://dictionary.casrai.org/Contributor_Roles/Methodology http://purl.org/credit/ontology f21e2be9-4e38-4ab7-8691-d6f72d5d5843 methodology role project administration role Management and coordination responsibility for the research activity planning and execution. https://orcid.org/0000-0001-5059-4132 program administration role http://dictionary.casrai.org/Contributor_Roles/Project_administration http://purl.org/credit/ontology a693fe76-ea33-49ad-9dcc-5e4f3ac5f938 project administration role resources role Provision of study materials, reagents, materials, patients, laboratory samples, animals, instrumentation, computing resources, or other analysis tools. https://orcid.org/0000-0001-5059-4132 resource provision role http://dictionary.casrai.org/Contributor_Roles/Resources http://purl.org/credit/ontology ebd781f0-bf79-492c-ac21-b31b9c3c990c resources role software role Programming, software development; designing computer programs; implementation of the computer code and supporting algorithms; testing of existing code components. https://orcid.org/0000-0001-5059-4132 software systems role http://dictionary.casrai.org/Contributor_Roles/Software http://purl.org/credit/ontology f89c5233-01b0-4778-93e9-cc7d107aa2c8 software role supervision role http://purl.obolibrary.org/obo/IAO_0000120 Oversight and leadership responsibility for the research activity planning and execution, including mentorship external to the core team. https://orcid.org/0000-0001-5059-4132 supervisory role http://dictionary.casrai.org/Contributor_Roles/Supervision http://purl.org/credit/ontology 0c8ca7d4-06ad-4527-9cea-a8801fcb8746 supervision role validation role http://purl.obolibrary.org/obo/IAO_0000120 Verification, whether as a part of the activity or separate, of the overall replication/reproducibility of results/experiments and other research outputs. https://orcid.org/0000-0001-5059-4132 http://dictionary.casrai.org/Contributor_Roles/Validation http://purl.org/credit/ontology 4b1bf348-faf2-4fc4-bd66-4cd3a84b9d44 validation role visualization role http://purl.obolibrary.org/obo/IAO_0000120 Preparation, creation and/or presentation of the published work, specifically visualization/data presentation. https://orcid.org/0000-0001-5059-4132 http://dictionary.casrai.org/Contributor_Roles/Visualization http://purl.org/credit/ontology 76b9d56a-e430-4e0a-84c9-59c11be343ae visualization role writing original draft role http://purl.obolibrary.org/obo/IAO_0000123 Preparation, creation and/or presentation of the published work, specifically writing the initial draft (including substantive translation). https://orcid.org/0000-0001-5059-4132 original draft preparation role http://dictionary.casrai.org/Contributor_Roles/Writing_%E2%80%93_original_draft http://purl.org/credit/ontology 43ebbd94-98b4-42f1-866b-c930cef228ca writing original draft role writing review and editing role http://purl.obolibrary.org/obo/IAO_0000123 Preparation, creation and/or presentation of the published work by those from the original research group, specifically critical review, commentary or revision – including pre- or post-publication stages. https://orcid.org/0000-0001-5059-4132 http://dictionary.casrai.org/Contributor_Roles/Writing_%E2%80%93_review_%26_editing http://purl.org/credit/ontology d3aead86-f2a2-47f7-bb99-79de6421164d writing review and editing role oboInOwl:Subset owl:Thing example to be eventually removed 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 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 term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term 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 Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated 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 Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot core placeholder removed An editor note should explain what were the merged terms and the reason for the merge. terms merged 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 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 This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. We expect to be able to mine these new reasons and add instances as required. other true 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 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 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 Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term 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 ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation axiom holds for all times This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about Contributor Role Ontology