BFO 2 Reference: BFO does not claim to provide complete coverage of entities of all types. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning - coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation. BFO 2 Reference: BFO's treatment of continuants and occurrents - as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality - earlier called the 'SNAP' and 'SPAN' perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science. BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. 'Entity' is an example of a primitive term. Primitive terms in a highest-level ontology such as BFO are terms that 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. Alan Ruttenberg Albert Goldfain Barry Smith Bill Duncan Bjoern Peters Chris Mungall David Osumi-Sutherland Fabian Neuhaus Holger Stenzhorn James A. Overton Janna Hastings Jie Zheng Jonathan Bona Larry Hunter Leonard Jacuzzo Ludger Jansen Mark Ressler Mathias Brochhausen Mauricio Almeida Melanie Courtot Pierre Grenon Randall Dipert Ron Rudnicki Selja Seppälä Stefan Schulz Thomas Bittner Werner Ceusters Yongqun "Oliver" He Jian Guan (关健) Jiangan Xie (谢江安) 2025-01-18 The Pathogen-related Informed Consent Ontology (PICO) is an ontology for the informed consent and informed consent process in the pathogen-related medical fields, especially for pathological data use. Pathogen-related Informed Consent Ontology (PICO：病原体相关知情同意本体) http://creativecommons.org/licenses/by/4.0/ PICO is an application ontology for the standardization of pathogen-related informed consent data and the classification of term logical relations. The current focus of PICO development is to represent different pathogenetic data use in such a way that it will support consistent representation of medical questionnaires. Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif. The BSD license on the BFO project site refers to code used to build BFO. This BFO 2.0 version represents a major update to BFO and is not strictly backwards compatible with BFO 1.1. The previous OWL version of BFO, version 1.1.1 will remain available at http://ifomis.org/bfo/1.1 and will no longer be updated. The BFO 2.0 OWL is a classes-only specification. The incorporation of core relations has been held over for a later version. https://github.com/PICO-ontology/PICO 1.0.0 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 label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status definition definition textual definition A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. 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> https://orcid.org/0000-0002-7702-4495 DEFINITION Allyson Lister 8.10.2019: Although the IAO definition has been included here, we have made a curation decision to allow non-Aristotelian definitions. definition definition textual 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> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note 1 editor_note editor note editor note definition editor term editor Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Peter McQuilton https://orcid.org/0000-0002-7702-4495 definition editor definition editor term editor term editor alternative label alternative term A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label alternative term alternative term alternative_term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Peter McQuilton https://orcid.org/0000-0002-7702-4495 definition source definition source definition_source curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg IAO:0000232 uberon curator_notes 1 curator_notes curator note curator note curator notes term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from imported from OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label elucidation has associated axiom(nl) has associated axiom(fol) has axiom label term_mapping_to_UMLS term_mapping_to_NCIT Cooper Stansbury This annotation property specifies classes that were developed as part of an alignment effort between the Common Rule Ontology and the Informed Consent Ontology in the Summer of 2018. These classes represent entities that are necessary for understanding the regularatory frameworks that influence informed consent, often at a different level of granularity than individual consent processes. These classes were created to be compatible with regulatory frameworks outside the Unitied States, hence they are general. RUBRIC An association that that connects a concept representing a GDC value to any associated GDC property concept(s). A32 Conceptual Entity Is_Value_For_GDC_Property Is_Value_For_GDC_Property Is_Value_For_GDC_Property An association specifying the Values for a specific OORO Prostate Cancer (PC) Attribute. A42 Conceptual Entity Has_OORO_PC_Value Has_OORO_PC_Value Has_OORO_PC_Value true A property representing a concept unique identifier within the NCI Enterprise Vocabulary Service's NCI Thesaurus. NHC0 Conceptual Entity code code code A property that represents a description of the sort of thing or category to which a concept belongs in the context of the UMLS semantic network. P106 Conceptual Entity Semantic Type Semantic_Type In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS. Semantic_Type Semantic_Type A property representing an alternative Preferred Name for use in some NCI systems. P107 Conceptual Entity Display Name Display_Name Display Name Display_Name Display_Name A property representing the word or phrase that NCI uses by preference to refer to the concept. P108 Conceptual Entity Preferred Name Preferred_Name Preferred Name Preferred Term Preferred_Name Preferred_Name A property representing the concept unique identifier (CUI) assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept. P207 Conceptual Entity UMLS CUI UMLS_CUI UMLS_CUI UMLS_CUI A property representing the concept unique identifier (CUI) for those concepts that appear in NCI Metathesaurus but not in the National Library of Medicine Unified Medical Language System (NLM UMLS). P208 Conceptual Entity NCI Metathesaurus CUI NCI_META_CUI NCI_META_CUI NCI_META_CUI A property used to flag terms that are part of an FDA data standard manual, including Route of Administration, Dosage Form, Package Type and Potency. P317 Conceptual Entity FDA Table FDA_Table FDA_Table FDA_Table A property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake. P322 Conceptual Entity Contributing Source Contributing_Source Contributing_Source Contributing_Source A property representing the English language definition of a concept from a source other than NCI. P325 Conceptual Entity [source] Definition ALT_DEFINITION ALT_DEFINITION ALT_DEFINITION true A property representing a retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding. P366 Conceptual Entity Legacy Concept Name Legacy Concept Name Legacy_Concept_Name Legacy Concept Name A property representing that a term in another terminology has been mapped to a term in NCIt and describes the relationship between the mapped terms. P375 Conceptual Entity Maps_To Maps_To Maps_To A property representing notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept. P98 Conceptual Entity DesignNote DesignNote DesignNote DesignNote ISA alternative term An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term An alternative term used by the IEDB. IEDB alternative term Oliver He Sam Smith US Standard Occupational Classification (SOC) ID https://www.bls.gov/oes/current/oes_stru.htm https://www.bls.gov/soc/ US SOC ID Jian Guan (关健) 2025-03-22T11:25:34Z 中文翻译 chinese translation S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S present in taxon Peter McQuilton 2019-10-17T13:38:16.742124Z alternative definition excluded_subClassOf true excluded subClassOf The guidelines for using names of persons or organizations as creators also apply to contributors. Typically, the name of a Contributor should be used to indicate the entity. 1999-07-02 An entity responsible for making contributions to the resource. Contributor A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/contributor) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation. Examples of a Creator include a person, an organization, or a service. Typically, the name of a Creator should be used to indicate the entity. 1999-07-02 An entity primarily responsible for making the resource. Creator A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/creator) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation. Date may be used to express temporal information at any level of granularity. Recommended practice is to express the date, date/time, or period of time according to ISO 8601-1 [[ISO 8601-1](https://www.iso.org/iso-8601-date-and-time-format.html)] or a published profile of the ISO standard, such as the W3C Note on Date and Time Formats [[W3CDTF](https://www.w3.org/TR/NOTE-datetime)] or the Extended Date/Time Format Specification [[EDTF](http://www.loc.gov/standards/datetime/)]. If the full date is unknown, month and year (YYYY-MM) or just year (YYYY) may be used. Date ranges may be specified using ISO 8601 period of time specification in which start and end dates are separated by a '/' (slash) character. Either the start or end date may be missing. 1999-07-02 A point or period of time associated with an event in the lifecycle of the resource. Date A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/date) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation. Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource. 1999-07-02 An account of the resource. Description A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/description) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation. Recommended practice is to identify the resource by means of a string conforming to an identification system. 1999-07-02 identifier_dc An unambiguous reference to the resource within a given context. Identifier identifier A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/identifier) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation. Recommended practice is to identify the related resource by means of a URI. If this is not possible or feasible, a string conforming to a formal identification system may be provided. 1999-07-02 A related resource. Relation relation A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/relation) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation. 1999-07-02 A name given to the resource. Title A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/title) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation. description is referenced by relation replaces subset created by creation date ID of merged class. has_alternative_id has broad synonym has_broad_synonym A property representing a reference to an identical or very similar object in another database. Reference database or publication source. Conceptual Entity xRef database_cross_reference has database cross reference xRef A property representing a fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. Exact synonym. Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 FULL_SYN Synonym with Source Data has exact synonym has exact synonym has_exact_synonym has narrow synonym has_narrow_synonym Name space of the ontology. disease_ontology has_obo_namespace Has related synonym. has related synonym has_related_synonym has synonym An identifier for an individual entity. An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. id An association that connects the concept defining a particular terminology subset with concepts that belong to this subset. In subset. Concept_In_Subset in subset in_subset shorthand Comment. comment comment is defined by label label A human readable name for this class. A human-readable name for the subject. label label see_also_rdf_schema see also equivalent property A skos concept mapping used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably. has exact match alternate name identifier_schema identifier library_of_congress_subject_headings Library of Congress Subject Headings http://purl.org/dc/terms/LCSH https://viaf.org/viaf/174475040 dewey_decimal_classification Dewey Decimal Classification library_of_congress_classification Library of Congress Classification follows follows nci_thesaurus_id NCI Thesaurus ID short_name short name viaf_id VIAF ID name name practiced_by practiced by medical_dictionary_for_regulatory_activities_id Medical Dictionary for Regulatory Activities ID mesh_descriptor_id Such as C004931 for DPPH or D008180 for systemic lupus erythematosus. MeSH Descriptor ID derived_from derived from has_cause has cause has part realizes is about is about has material basis in has specified input has_specified_input has specified output is_specified_output_of achieves_planned_objective concretizes in taxon transmitted by disease caused by disruption of disease has basis in disruption of disease causes disruption of disease disrupts disease has location requires/improves personal attribute supports implementation of contributes to the implementation of competency gained through has quality is about realizes is manifestation of describes has unique identifier has value 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 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 (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]) 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] BFO:0000003 occurrent Occurrent BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] BFO:0000004 ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] BFO:0000006 s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] BFO:0000008 t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] BFO:0000009 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] BFO:0000011 st-region SpatiotemporalRegion the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] BFO:0000015 process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] BFO:0000016 disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] BFO:0000017 realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] BFO:0000018 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] BFO:0000019 quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] BFO:0000020 sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella 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:0000023 role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] BFO:0000024 fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] BFO:0000026 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] BFO:0000027 object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] BFO:0000028 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] BFO:0000029 site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] BFO:0000030 object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) BFO:0000031 gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] BFO:0000034 function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] BFO:0000035 p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] BFO:0000038 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] BFO:0000040 material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] BFO:0000140 cf-boundary ContinuantFiatBoundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] BFO:0000141 immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity BFO:0000142 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] BFO:0000144 process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] BFO:0000145 r-quality RelationalQuality 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. a marriage bond, an instance of requited love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] BFO:0000146 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] BFO:0000147 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] BFO:0000148 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] BFO:0000182 history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) A disease that is the consequence of the presence of pathogenic microbial agents, including pathogenic viruses, pathogenic bacteria, fungi, protozoa, multicellular parasites, and aberrant proteins known as prions. infectious disease DOID:10115 DOID:11078 DOID:1304 DOID:1321 DOID:2040 DOID:2288 DOID:3099 DOID:4120 DOID:4620 DOID:5256 DOID:945 DOID:95 DOID:9532 DOID:9696 ICD9CM:079.0 UMLS_CUI:C0001485 infectious disease disease_ontology DOID:0050117 DO:wk disease by infectious agent DOID:0050117 A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. MESH:D004194 NCI:C2991 SNOMEDCT_US_2023_03_01:64572001 UMLS_CUI:C0012634 disease_ontology DOID:4 disease DOID:4 A Human immunodeficiency virus infectious disease that results_in reduction in the numbers of CD4-bearing helper T cells below 200 per microliter of blood or 14% of all lymphocytes thereby rendering the subject highly vulnerable to life-threatening infections and cancers, has_material_basis_in Human immunodeficiency virus 1 or has_material_basis_in Human immunodeficiency virus 2, which are transmitted_by sexual contact, transmitted_by transfer of blood, semen, vaginal fluid, pre-ejaculate, or breast milk, transmitted_by congenital method, and transmitted_by contaminated needles. Opportunistic infections are common in people with AIDS. EFO:0000765 ICD10CM:B20 MESH:D000163 NCI:C2851 SNOMEDCT_US_2023_03_01:62479008 UMLS_CUI:C0001175 AIDS acquired Immune deficiency disease_ontology acquired immune deficiency syndrome DOID:635 acquired immunodeficiency syndrome MESH:D000163 DOID:635 GSSO:000492 Information content entity that is an empirical result found to be meaningful to one or more person(s) or a community, such that it can be interpreted by them in ways that they value, and which arises from a systematic analytic and/or deliberative process of investigation and study of other information content entities, that are often, but not exclusively other data item(s), thereby accounting for those other information content entities. knowledge entity knowledge content entity knowledge content entities 1 knowledge content knowledge GSSO:000526 Diseases transmitted or propagated by sexual conduct. http://purl.obolibrary.org/obo/MONDO_0021681 https://homosaurus.org/terms/STDs other venereal disease venereal disease venereal disease NOS venereal disease, unspecified sexually transmitted diseases and infections‎ other sexually transmitted disease unspecified sexually transmitted disease sexually transmitted infectious disease sexsygdomme sexually transmitted disease seksuelt overførte sygdomme sexually transmitted diseases http://homosaurus.org/v2/STDs http://id.loc.gov/authorities/subjects/sh85142634 RA644.V4 RC200-RC203 STD STD http://purl.bioontology.org/ontology/MEDDRA/10040490 http://purl.bioontology.org/ontology/MESH/D012749 GSSO:002345 A branch of knowledge. area of knowledge content area field of knowledge knowledge field knowledge fields http://purl.obolibrary.org/obo/NCIT_C70772 field GSSO:002346 Fields of inquiry in human constructs and concerns as opposed to natural processes and social relations. These are traditionally the study of literature, philosophy, and religion. https://en.wikipedia.org/wiki/Category:Humanities https://en.wikipedia.org/wiki/Humanities https://en.wikipedia.org/wiki/Outline_of_the_humanities the humanities humanities http://id.loc.gov/authorities/subjects/sh85062913 AZ http://purl.bioontology.org/ontology/MESH/D006809 GSSO:002368 Humanities fields that form the basis of humanities studies; i.e. non-applied humanities. basic humanities basic GSSO:003081 A branch of philosophy that involves systematizing, defending, and recommending concepts of right and wrong conduct. The field of ethics, along with aesthetics, concerns matters of value, and thus comprises the branch of philosophy called axiology. https://homosaurus.org/terms/ethics https://en.wikipedia.org/wiki/Ethics moral philosophy ethics http://id.loc.gov/authorities/subjects/sh85045096 170 BJ http://purl.obolibrary.org/obo/NCIT_C39796 http://purl.bioontology.org/ontology/MESH/Q000941 GSSO:003088 Philosophy fields that form the basis of philosophy; i.e. non-applied philosophies. basic philosophy basic philosophies GSSO:003238 A proposition or value that is a guide for behavior or evaluation. https://en.wikipedia.org/wiki/Category:Principles https://en.wikipedia.org/wiki/Principle principle principles GSSO:003239 Principles which provide a framework within which ethical dilemmas and other problems may be analyzed. https://en.wikipedia.org/wiki/Category:Ethical_principles principle of ethics ethical principle ethical principles GSSO:003291 Legal, social, or ethical principles of freedom or entitlement; that is, rights are the fundamental normative rules about what is allowed of people or owed to people, according to some legal system, social convention, or ethical theory. https://mamoura.eci.ufmg.br/tematres/vocab/index.php?tema=120 https://en.wikipedia.org/wiki/Category:Rights https://en.wikipedia.org/wiki/Rights right rettigheder rights GSSO:003292 Moral principles or norms that describe certain standards of human behaviour and are regularly protected as natural and legal rights in municipal and international law. They are commonly understood as inalienable,[3] fundamental rights "to which a person is inherently entitled simply because she or he is a human being" and which are "inherent in all human beings", regardless of their nation, location, language, religion, ethnic origin, or any other status. https://mamoura.eci.ufmg.br/tematres/vocab/index.php?tema=62 https://en.wikipedia.org/wiki/Category:Human_rights https://en.wikipedia.org/wiki/Human_rights human right human rights menneskerettigheder http://homosaurus.org/v2/humanRights http://id.loc.gov/authorities/subjects/sh85026379 JC571-JC628 K3236-K3268.5 http://purl.bioontology.org/ontology/MESH/D006806 GSSO:003294 The ability of an individual or group to seclude themselves, or information about themselves, and thereby express themselves selectively. The boundaries and content of what is considered private differ among cultures and individuals. https://en.wikipedia.org/wiki/Category:Privacy https://en.wikipedia.org/wiki/Privacy privacy right right to privacy privacy http://id.loc.gov/authorities/subjects/sh85107027 BF637.P74 http://purl.bioontology.org/ontology/MESH/D018907 GSSO:003756 The practical application of moral considerations. It is ethics with respect to real-world actions and their moral considerations in the areas of private and public life, the professions, health, technology, law, and leadership. https://en.wikipedia.org/wiki/Applied_ethics https://en.wikipedia.org/wiki/Category:Applied_ethics https://www.wikidata.org/wiki/Q538733 applied ethics http://id.loc.gov/authorities/subjects/sh93005640 172-179 GSSO:003848 The intellectual and practical activity encompassing the systematic study of the structure and behaviour of the physical and natural world through observation and experiment. The study of natural phenomena by observation, measurement, and experimentation. https://en.wikipedia.org/wiki/Category:Science https://en.wikipedia.org/wiki/Science scientific science sciences http://id.loc.gov/authorities/subjects/sh85118553 500 Q http://purl.obolibrary.org/obo/NCIT_C61397 http://purl.bioontology.org/ontology/MESH/D012586 GSSO:003850 The development of scientific knowledge and predictions, principally in natural sciences but also in other empirical sciences, which are used as the scientific foundation for applied science. Basic science develops and establishes information to predict phenomena and perhaps to understand nature. basic science basic sciences GSSO:004917 A process for getting permission before conducting a health care intervention on a person, or for disclosing personal information. A health care provider may ask a patient to consent to receive therapy before providing it, or a clinical researcher may ask a research participant before enrolling that person into a clinical trial. Informed consent is collected according to guidelines from the fields of medical ethics and research ethics. Consent by a patient to a surgical or medical procedure or participation in a clinical study after achieving an understanding of the relevant medical facts and the risks involved. Voluntary authorization, by a patient or research subject, with full comprehension of the risks involved, for diagnostic or investigative procedures, and for medical and surgical treatment. https://en.wikipedia.org/wiki/Informed_consent https://www.wikidata.org/wiki/Q764527 This term is also used in other contexts, such as in social scientific research, when participants are asked to affirm that they understand the research procedure and consent to it, or in sex, where informed consent means each person engaging in sexual activity is aware of any positive statuses (for sexually transmitted infections and/or diseases) they might expose themselves to. informed consent http://id.loc.gov/authorities/subjects/sh85066306 http://purl.obolibrary.org/obo/NCIT_C16735 http://purl.bioontology.org/ontology/MESH/D007258 GSSO:009049 A branch of science studying formal language disciplines concerned with formal systems, such as logic, mathematics, statistics, theoretical computer science, artificial intelligence, information theory, game theory, systems theory, decision theory, and theoretical linguistics. https://en.wikipedia.org/wiki/Category:Formal_sciences https://en.wikipedia.org/wiki/Formal_science https://www.wikidata.org/wiki/Q816264 formal science formal sciences GSSO:009671 The study of the ethical issues emerging from advances in biology and medicine. It is also moral discernment as it relates to medical policy and practice. Bioethics are concerned with the ethical questions that arise in the relationships among life sciences, biotechnology, medicine and medical ethics, politics, law, theology and philosophy. life sciences ethics https://en.wikipedia.org/wiki/Bioethics https://en.wikipedia.org/wiki/Category:Bioethics https://www.wikidata.org/wiki/Q194294 health care ethics biomedical ethics bioethics biological ethics http://id.loc.gov/authorities/subjects/sh85014136 QH332 http://purl.obolibrary.org/obo/NCIT_C16340 http://purl.bioontology.org/ontology/MESH/D001675 GSSO:009828 Any of various rights which relate to the communication, collection, access, use, and control of information. right to information information right information rights GSSO:011171 The study of the structure, algorithms, behavior, and interactions of natural and artificial computational systems. https://en.wikipedia.org/wiki/Informatics https://www.wikidata.org/wiki/Q4027615 informatics http://purl.obolibrary.org/obo/NCIT_C18145 http://purl.bioontology.org/ontology/MESH/D048088 GSSO:011173 An interdisciplinary field that uses scientific methods, processes, algorithms and systems to extract knowledge and insights from noisy, structured and unstructured data, and apply knowledge and actionable insights from data across a broad range of application domains. https://en.wikipedia.org/wiki/Data_science https://www.wikidata.org/wiki/Q2374463 data science data sciences http://purl.bioontology.org/ontology/MESH/D000077488 GSSO:011174 The development of informatics knowledge and predictions, principally in natural sciences but also in other empirical sciences, which are used as the scientific foundation for applied informatics. Basic informatics develops and establishes information to predict phenomena and perhaps to understand nature. basic informatics IAO:0000001 conditional specification A directive information entity that specifies what should happen if the trigger condition is fulfilled. PlanAndPlannedProcess Branch OBI branch derived OBI_0000349 conditional specification IAO:0000027 data item Data items include counts of things, analyte concentrations, and statistical summaries. 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 information content entity IAO:0000033 An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity IAO:0000055 rule example to be added A rule is an executable which guides, defines, restricts actions. MSI PRS OBI_0500021 PRS rule IAO:0000064 algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. Philippe Rocca-Serra PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm IAO:0000078 curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification IAO:0000102 data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part IAO:0000104 plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg Clint Dowland OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 IAO:0000310 document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document ICO:0000065 A study that is a clinical trial that requires an informed consent process. Elizabeth Eisenhauer, Yongqun He Based on NCI/PT, a clinical trial is a type of research study that tests how well new medical approaches work in people. These studies test new methods of screening, prevention, diagnosis, or treatment of a disease. Needs work. Best fit is to rely on SIO_0001000, which has a fine-grained hierarchy. Parent is 'intervention study' (SIO_0000994) which is an investigation (SIO_0000747). However, we have investigation already defined in OBI_0000066. clinical trial UMLS: C0008976 ICO:0000078 A risk is a disposition or the potential future harm that may arise from some present action. It is often combined or confused with the probability of an event which is seen as undesirable. This term definition is adapted from the NCIt definiton of "Risk" (C17102) . The following source is alos referenced: BMEO(Biomedical Ethics Ontology) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2725426/ Asiyah Yu Lin, Marcy Harris, Yongqun He, Elizabeth Eisenhauer, Alla Karnovsky, Frank Manion NCIt: C17102 This class is under group discussion as of 03/26/2019. C0035647 C17102 risk ICO:0000288 A woman who is pregnant. Could reuse: http://purl.obolibrary.org/obo/ontoneo/ONTONEO_00000197 pregnant woman ICO:0000289 A role inhering in a Homo sapiens that is realized in a process of incarceration. Cooper Stansbury, Jonathan Vajda Note from Jonathan Vajda: Depending on the level of granluarity, we could have prisoner role, incarcerated role, etc. and these roles would differentiated by what kind of stasis of incarceration necessary. prisoner role A disorder characterized by behavioral and/or psychological abnormalities, often accompanied by physical symptoms. The symptoms may cause clinically significant distress or impairment in social and occupational areas of functioning. Representative examples include anxiety disorders, cognitive disorders, mood disorders and schizophrenia. DOID:150 MESH:D001523 MFOMD:0000004 NCIT:C2893 SCTID:74732009 Psychiatric disease Psychiatric disorder disease of mental health mental disorder mental dysfunction mental illness MONDO:0002025 psychiatric disorder MONDO:0002025 A melancholy feeling of sadness and despair. DOID:1596 ICD10CM:F32 ICD9:311 MEDGEN:4229 MESH:D003866 MFOMD:0000013 NCIT:C2982 SCTID:35489007 UMLS:C0011581 depression mental depression melancholia melancholias syndrome, depressive syndromes, depressive MONDO:0002050 depressive disorder MONDO:0002050 A disease involving the central nervous system. DOID:331 EFO:0009386 MEDGEN:892343 MESH:D002493 NCIT:C2934 SCTID:23853001 UMLS:C4021765 CNS disorder central nervous disease central nervous system disease central nervous system disease or disorder central nervous system disorder disease of central nervous system disease of the central nervous system disease or disorder of central nervous system disorder of central nervous system MONDO:0002602 central nervous system disorder MONDO:0002602 A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves. DOID:863 EFO:0000618 ICD10CM:G00-G99 ICD9:349.89 ICD9:349.9 MEDGEN:14336 MESH:D009422 NCIT:C26835 SCTID:118940003 UMLS:C0027765 Wikipedia:Nervous_system_disease disease of nervous system disease or disorder of nervous system disorder of nervous system nervous system disease nervous system disease or disorder nervous system disorder neurologic disease neurologic disorder neurological disease neurological disorder MONDO:0005071 'psychiatric disorder' is not classified as a 'nervous system disorder' in Mondo (though it is often as such): the hallmarks of psychiatric disorders are based in behavior and emotional state, and the relation with nervous system malfunction or damage is not always clearly determined. nervous system disorder MONDO:0005071 A disease that has its basis in the disruption of mental process. EFO:0000677 ICD9:290-299.99 ICD9:298.8 ICD9:V11.9 MEDGEN:14047 MESH:D001523 NCIT:C2893 NIFSTD:birnlex_12669 SCTID:74732009 UMLS:C0004936 disorder of mental process mental or behavioral disorder mental or behavioural disorder mental process disease MONDO:0005084 mental disorder MONDO:0005084 A major psychotic disorder characterized by abnormalities in the perception or expression of reality. It affects the cognitive and psychomotor functions. Common clinical signs and symptoms include delusions, hallucinations, disorganized thinking, and retreat from reality. https://github.com/monarch-initiative/mondo/issues/4521 schizophrenia (disease) schizophrenia 12 DOID:5419 HP:0100753 ICD9:295 ICD9:295.8 ICD9:295.80 ICD9:295.85 ICD9:295.9 ICD9:295.90 MEDGEN:48574 NCIT:C3362 NIFSTD:birnlex_2104 OMIM:181500 Orphanet:3140 SCTID:58214004 UMLS:C0036341 icd11.foundation:1683919430 schizophrenia schizophrenia (disease) schizophrenia-1 SCZD schizoaffective disorder schizophrenia with or without an affective disorder schizophrenia, susceptibility to MONDO:0005090 schizophrenia MONDO:0005090 A cognitive disorder a disturbance in which the person's mood is hypothesized to be the main underlying feature. DOID:3324 EFO:0004247 ICD10CM:F30-F39 ICD9:296.99 MEDGEN:99866 MESH:D019964 NCIT:C92200 SCTID:46206005 UMLS:C0525045 episodic mood disorder MONDO:0005371 mood disorder MONDO:0005371 An abnormal condition of the mind that involves a loss of contact with reality. People experiencing psychosis may exhibit personality changes and thought disorder. Depending on its severity, this may be accompanied by unusual or bizarre behavior, as well as difficulty with social interaction and impairment in carrying out daily life activities. mental or behavioral disorder mental or behavioural disorder DOID:2468 EFO:0005407 HP:0000709 ICD9:298.8 ICD9:298.9 MEDGEN:19568 NCIT:C78576 SCTID:69322001 UMLS:C0033975 psychosis MONDO:0005485 psychotic disorder MONDO:0005485 A disease affecting the brain or part of the brain. DOID:936 EFO:0005774 ICD9:348.3 ICD9:348.30 ICD9:348.8 ICD9:348.9 MEDGEN:14214 MESH:D001927 NCIT:C96413 SCTID:81308009 UMLS:C0006111 brain disease brain disease or disorder disease of brain disease or disorder of brain disorder of brain encephalopathy MONDO:0005560 Editor note: NCIT has different classes for brain disease and encephalopathy brain disorder MONDO:0005560 https://github.com/monarch-initiative/mondo/issues/5858 human disease or disorder MONDO:0700096 human disease MONDO:0700096 NCIT:C103270 The release from the requirement to obtain informed consent during a study that is granted by Human Subject Protection committee for a research institution for a protocol that is being reviewed by the Institutional Review Board. C103270 Governmental or Regulatory Activity Consent Waiver C3641166 GDC Consent Waiver Consent Waiver Waiver Of Informed Consent Consent Waiver NCIT:C113644 An identifying designation assigned to an individual that corresponds with their function. C113644 Qualitative Concept Person Role Title C1519530 CareLex An identifying designation assigned to an individual that corresponds with their function. May include but not limited to Principal Investigator, SubInvestigator, Study Coordinator, Sponsor Project Manager, CRO Project Manager, Data Manager. Person Role Person Role Title Role Title Title title Person Role Title NCIT:C16309 Artificial intelligence is the branch of computer science that deals with writing computer programs that can solve problems creatively. C16309 Occupational Activity Artificial Intelligence C0003916 CDISC-GLOSS A system's ability to correctly interpret external data, to learn from such data, and to use those learnings to achieve specific goals and tasks through flexible adaptation. [Kaplan, A; Haenlein, M (1 January 2019) Business Horizons; IEEE-USA POSITION STATEMENT. Artificial Intelligence Research, Development & Regulation Adopted by the IEEE-USA, Board of Directors (February 2017)] See also machine learning, deep learning, natural language processing, synthetic data. Artificial_Intelligence Artificial Intelligence artificial intelligence (AI) Artificial Intelligence NCIT:C16423 An age group comprised of individuals who are not yet an adult. The specific cut-off age will vary by purpose. C16423 Age Group Child C0008059 FDA NICHD Children CHILD Child Children Children (0-21) Child NCIT:C165830 Data relating to patient health status and/or the delivery of health care routinely collected from sources other than traditional clinical trials. Examples of sources include data derived from electronic health records (EHRs); medical claims and billing data; data from product and disease registries; patient-generated data, including from in-home-use settings; and data gathered from other sources that can inform on health status, such as mobile devices. (21 U.S.C. 355g(b)).5 and Framework for FDA's Real-World Evidence Program December 2018) C165830 Idea or Concept Real-world Data CL979052 CDISC CDISC-GLOSS MRCT-Ctr Data relating to patient health status and/or the delivery of health care routinely collected from sources other than traditional clinical trials. NOTE: Examples of sources include data derived from electronic health records (EHRs); medical claims and billing data; data from product and disease registries; patient-generated data, including from in-home-use settings; and data gathered from other sources that can inform on health status, such as mobile devices. [After 21 U.S.C. 355g(b)).5 and Framework for FDA's Real-World Evidence Program December 2018; FDA Draft Guidance, Data Standards for Drug and Biological Product Submissions Containing Real-World Data, OCTOBER 2021] See also Real-World Evidence (RWE) Data relating to patient health status and/or the delivery of health care routinely collected from sources other than traditional clinical trials. NOTE: Examples of sources include data derived from electronic health records (EHRs); medical claims and billing data; data from product and disease registries; patient-generated data, including from in-home-use settings; and data gathered from other sources that can inform on health status, such as mobile devices. [After 21 U.S.C. 355g(b)).5 and Framework for FDA's Real-World Evidence Program December 2018] See also Real-World Evidence (RWE) Health-related information collected from many different types of records and used for research purposes. (https://mrctcenter.org/glossaryterm/real-world-data-rwd/) RWD Real World Data Real World Data (RWD) Real-World Data (RWD) Real-world Data Real-world Data NCIT:C16669 The state of a subject's mental or physical condition. C16669 Organism Attribute Health Status C0018759 CDISC The state of a subject's mental or physical condition. Health_Status General Health Status Health Status Health Status NCIT:C17005 A group of individuals united by a common factor (e.g., geographic location, ethnicity, disease, age, gender) C17005 Population Group Population Group C1257890 CDISC-GLOSS Any finite or infinite collection of subjects from which a sample is drawn for a study to obtain estimates for values that would be obtained if the entire population were sampled. [AMA style Manual] Population_Group Group Population Population Group Subpopulation population Population Group NCIT:C18465 The branch of ethics that studies moral values in research sciences and practices. C18465 Occupation or Discipline Research Ethics C0814851 Research_Ethics Research Ethics Research Ethics NCIT:C19067 An identifying designation. C19067 Qualitative Concept Title C3888414 BRIDG Title Title title Title NCIT:C19332 The distinguishing qualities or prominent aspects of an individual person. C19332 Organism Attribute Personal Attribute C0681884 Personal_Attribute Personal Personal Attribute Subject Characteristics Personal Attribute NCIT:C20181 An organizational header for concepts representing mostly abstract entities. C20181 Classification Conceptual Entity C1254372 Conceptual_Entities Conceptual Entity Conceptual Entity NCIT:C20587 Subgroups of populations based on age. C20587 Population Group Age Related Group C0027362 Age_Group Age Group Age Related Group Age Related Group NCIT:C21007 Any physical or mental impairment that interferes with an individual's ability to perform desired activities. C21007 Organism Attribute Disability C0231170 Patient Code (Appendix B) FDA OORO Any physical or mental impairment that interferes with an individual's ability to perform desired activities. High level categorizations of disabilities having an impact on basic functioning. This is important for research and health care policy using social determinants of health (SDOH). Values should be as identified by patient. Disability IMDRF:F1202 DISABILITY Disability Handicap Infirmity Disability NCIT:C25387 The positive effects of something. C25387 Idea or Concept Benefit C0814225 Benefits Benefit Benefits Benefit NCIT:C25460 Permission to do something. C25460 Conceptual Entity Consent C1511481 Consent Consent Consent NCIT:C25688 A condition or state at a particular time. C25688 Qualitative Concept Status Status C0449438 CTRP Status Status Status NCIT:C25712 A numerical quantity measured or assigned or computed. C25712 Conceptual Entity Value C1522609 BRIDG Value Value value Value NCIT:C41009 A term that helps define and render a concept unique. C41009 Conceptual Entity Qualifier C1514623 Qualifier Modifier Qualifier Qualifier NCIT:C41192 Decision of the competent authorities in form of a letter, document, or verbal or electronic form, that confirms that somebody has permission to do something or be somewhere, e.g. to realize a given project. C41192 Governmental or Regulatory Activity Authorization C1524004 CDISC-GLOSS The process of giving someone permission to do or have something. In multi-user computer systems, a system administrator defines for the system which users are allowed access to the system and what privileges of use are permitted. [HL7 EHR-S FM Glossary of Terms, 2010]. Authorization Allowance Authorization Authorized Permission authorization Authorization NCIT:C43359 Any number of entities (members) considered as a unit. C43359 Group Group C0441833 Group Group Panel Group NCIT:C45970 Removal of text elements that would make data individually identifiable. C45970 Activity Deidentification C1707660 CDISC-GLOSS The process of removing potentially identifying data or data elements to render data into a form that does not identify individuals and where identification is not likely to take place. NOTE: A general term for a process of removing the association between a set of identifying data and the data subject. Examples of potentially identifying data include name, birth date, social security number, home address, telephone number, e-mail address, medical record numbers, health plan beneficiary numbers, full-face photographic images). [After ISO/TS 25237: 2008 - Health Informatics - Pseudonymization; HIPAA: 45 CFR, 164.514] See also anonymization. Deidentification DID Deidentification de-identification Deidentification NCIT:C49100 The information contained in a data field. It may represent a numeric quantity, a textual characterization, a date or time measurement, or some other state, depending on the nature of the attribute. C49100 Conceptual Entity Data Value C1704610 Data_Value Data Value Data Value NCIT:C71754 Having no known name or identity or known source. C71754 Qualitative Concept Anonymous C2346787 Anonymous Anonymous Anonymous NCIT:C75906 A means of finding a solution to a problem, or a means of finding agreement or harmony. C75906 Conceptual Entity Resolution C2699488 DIPG/DMG Solution_Resolution Complete resolution Resolution Resolve Resolved Solution Resolution OBCS:0000058 A data item that measures the proportion of actual positives which are correctly identified as such (e.g. the percentage of sick people who are correctly identified as having the condition). Yongqun He sensitivity estimate true positive rate, recall WEB: http://en.wikipedia.org/wiki/Sensitivity_and_specificity STATO:0000233 sensitivity OBCS:0000233 A data item that is produced as the output of a data transformation. Person: Jie Zheng, Oliver He transformed data item OBI:0000011 planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process OBI:0000066 investigation Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS study investigation OBI:0200000 data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors data transformation OBI:1110040 infectious disease is a disease caused by an infectious agent IEDB IEDB infectious disease OCCO:00000003 A learned capability to perform an action with determined results with good execution often within a given amount of time, energy, or both. Oliver He Sam Smith https://en.wikipedia.org/wiki/Skill skill OCCO:00000004 A capability that an agent has to power the performance of various actions. Oliver He Sam Smith https://en.wikipedia.org/wiki/Ability ability OCCO:00000011 A disposition that can be evaluated on the basis of how well they are realized. They differ from functions in that their realizations are not the rationale – not the primary reason – for the existence of their bearers. Barry Smith David Limbaugh Eric Merrell Peter Koch https://philpapers.org/rec/MERC-14 capability OCCO:00000036 A skill realized in bringing others together and trying to reconcile differences. Oliver He Sam Smith https://www.onetonline.org/skills/soft/ 2.B.1.d negotiation OGMS:0000063 The totality of all processes through which a given disease instance is realized. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:55:44Z disease course OGMS:0000064 A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:56:26Z 10212020 for definition use: http://purl.obolibrary.org/obo/PATO_0001863 chronic disease course OGMS:0000123 A data item that is about a patient and is the specified output of a health care process assay or diagnostic process creation date: 2018-11-27 clinical data item ONS:0000091 A class which groups the data item collected as results from the analysis performed with an omics platform ENPADASI_WP4 omics data OPMI:0000093 information associated with an individual Oliver He https://www.oic.qld.gov.au/guidelines/for-government/access-and-amendment/introduction-to-the-acts/what-is-personal-information personal information PICO:0000001 Data and its information recorded electronically or in otherwise format, which can be identified to the special individual alone or in combination with other information. Data on persons (identity or reflecting their specific activities). TEAM GUIDELINES 个体水平数据 Jian Guan (关健) 2025-03-22T11:05:30Z individual-level data PICO:0000002 Information that once leaked, illegally provided or abused, personal information that may endanger the safety of the person and property, and can easily lead to damage to personal reputation, physical and mental health or discriminatory treatment. TEAM GUIDELINES 敏感个人信息 Jian Guan (关健) 2025-03-22T11:14:30Z sensitive personal information PICO:0000003 Data that have been collected from researches or routine clinical work and being stored for future use. TEAM GUIDELINES 现有数据 Jian Guan (关健) 2025-03-22T11:16:52Z stored data existing data PICO:0000005 The data which has not yet been consolidated. 松散数据 Jian Guan (关健) 2025-03-22T11:28:34Z unconsolidated data PICO:0000006 Information that once leaked, illegally provided or abused, personal information that may endanger the safety of the person and property, and can easily lead to damage to personal reputation, physical and mental health or discriminatory treatment. TEAM GUIDELINES 个人健康信息 Jian Guan (关健) 2025-03-22T11:34:15Z personal health information PICO:0000007 Data processing rule is a rule for data processing. 数据处理规则 Jian Guan (关健) 2025-03-22T11:44:34Z data processing rule PICO:0000008 Personal information processing rule is a rule for personal information processing. 个人信息处理规则 Jian Guan (关健) 2025-03-22T11:47:26Z personal information processing rule PICO:0000009 Data that with personal genetic or genomic information contains genetic privacy information that can be reversed Through bio-informatics analysis. 遗传信息 Jian Guan (关健) 2025-03-22T11:50:37Z genetic information PICO:0000010 Data that are produced and collected through basic research, applied research, and experimental development (collectively known as research), and through observation monitoring, investigation, and testing (not research). They are original and derived data used for scientific research activities or solving science problems in the field of medicine and the fusion of medical and other sciences. 医学科学数据 Jian Guan (关健) 2025-03-22T12:03:31Z medical scentific data PICO:0000011 Public health data is any data "related to publi health conditions, reproductive outcomes, causes of death, and quality of life". https://en.wikipedia.org/wiki/Health_data 公共卫生数据 Jian Guan (关健) 2025-03-22T12:06:09Z public health data health-related scientific data PICO:0000012 Article linked data is the data that come from public articles. 论文关联数据 Jian Guan (关健) 2025-03-22T23:59:23Z article linked data PICO:0000013 Data (usually datasets, or database) that can support the research purpose, materials and methods, as well as can resulted in the results, conclution of an article by data analysis. 论文关联核心数据 Jian Guan (关健) 2025-03-23T00:02:43Z article linked core data article supporting data PICO:0000014 The process of generating data. 数据生成 Jian Guan (关健) 2025-03-23T00:08:04Z data creating data generation PICO:0000015 An act of putting data to use. 数据应用 Jian Guan (关健) 2025-03-23T00:11:03Z data application data use PICO:0000016 To convey data from one person, place, or situation to another. https://en.wikipedia.org/wiki/Data_communication 数据转移 Jian Guan (关健) 2025-03-23T00:13:21Z data transfer PICO:0000017 To use data again especially in a different way or after reclaiming or reprocessing. 数据再利用 Jian Guan (关健) 2025-03-23T00:15:15Z data reusing PICO:0000018 Data exchange is the process of taking data structured under a source schema and transforming it into a target schema, so that the target data is an accurate representation of the source data. Data exchange allows data to be shared between different computer programs. https://en.wikipedia.org/wiki/Data_exchange 数据交换 Jian Guan (关健) 2025-03-23T00:20:08Z data exchange PICO:0000019 Big data analysis include capturing data, data storage, data analysis, search, sharing, transfer, visualization, querying, updating, information privacy, and data source. https://en.wikipedia.org/wiki/Big_data 大数据分析 Jian Guan (关健) 2025-03-23T00:22:26Z big data analysis PICO:0000020 (a) Stakeholder (corporate), a group, corporate, organization, member, or system that affects or can be affected by an organization's actions. (b) Project stakeholder, a person, group, or organization with an interest in a project. https://en.wikipedia.org/wiki/Stakeholder 利益相关者；干系人 Jian Guan (关健) 2025-03-23T00:29:42Z stakeholder PICO:0000021 An organization or person that processes data. 数据干系人 Jian Guan (关健) 2025-03-23T00:31:49Z data stakeholder PICO:0000022 An organization or an individual that independently decide the purpose and method of processing in practice of personal information processing activities. 个人信息处理者 Jian Guan (关健) 2025-03-23T00:35:42Z personal information processor PICO:0000023 An institution or an individual that have medical scientific data and have qualifications and/ or right to decide share with a third party institutions or researchers. 数据持有者 Jian Guan (关健) 2025-03-23T00:37:19Z data holder PICO:0000024 The action, process, or occupation of risk supervising,especially by a department. 风险监管 Jian Guan (关健) 2025-03-23T00:48:38Z risk supervision PICO:0000025 Free availability to the literature or data on the public internet, permitting any users to read, download, copy, distribute, print, search, and / or link to the full texts of these articles, datasets, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. https://en.wikipedia.org/wiki/Open_access 开放获取 Open access (OA) is a set of principles and a range of practices through which nominally copyrightable publications are delivered to readers free of access charges or other barriers.[1] With open access strictly defined (according to the 2001 definition), or libre open access, barriers to copying or reuse are also reduced or removed by applying an open license for copyright, which regulates post-publication uses of the work. Jian Guan (关健) 2025-03-23T00:50:13Z open access PICO:0000026 Hierarchical storage management (HSM), also known as tiered storage, is a data storage and data management technique that automatically moves data between high-cost and low-cost storage media. https://en.wikipedia.org/wiki/Hierarchical_storage_management 分级管理 Jian Guan (关健) 2025-03-23T00:54:09Z hierarchical management PICO:0000027 Big data ethics, also known simply as data ethics, refers to systemizing, defending, and recommending concepts of right and wrong conduct in relation to data, in particular personal data. https://en.wikipedia.org/wiki/Big_data_ethics 数据伦理 Jian Guan (关健) 2025-03-23T01:00:57Z data ethics PICO:0000028 PHI sensitivity is the control of access to information or knowledge that might result in loss of an advantage or level of security if disclosed to others. https://en.wikipedia.org/wiki/Information_sensitivity 个人健康信息敏感性 Jian Guan (关健) 2025-03-23T01:12:47Z personal health information sensitivity PHI sensitivity PICO:0000029 A common disease is a disease that mild and frequently. 常见疾病 Jian Guan (关健) 2025-03-23T01:17:30Z common disease PICO:0000030 A health examination record is a health record where health data and other information related to the care of a patient is maintained by the patient. https://en.wikipedia.org/wiki/Personal_health_record 健康体检记录 Jian Guan (关健) 2025-03-23T01:32:49Z health examination record personal health record (PHR) PICO:0000031 A severe sexually transmitted disease is is an severe infection that is spread by sexual activity, especially vaginal intercourse, anal sex, oral sex, or sometimes manual sex. https://en.wikipedia.org/wiki/Sexually_transmitted_infection 严重性传播疾病 Jian Guan (关健) 2025-03-23T01:39:02Z severe sexually transmitted disease PICO:0000032 Severe psychological disorder is a behavioral or mental pattern that causes significant distress or impairment of personal functioning. https://en.wikipedia.org/wiki/Mental_disorder 严重心理障碍 Jian Guan (关健) 2025-03-23T01:49:27Z severe psychological disorder PICO:0000033 An affective disturbance is any of a group of conditions of mental and behavioral disorder where the main underlying characteristic is a disturbance in the person's mood. https://en.wikipedia.org/wiki/Mood_disorder 情感障碍 Jian Guan (关健) 2025-03-23T01:51:27Z affective disturbance affective disorder PICO:0000034 Severe depression also known as clinical depression, is a mental disorder characterized by at least two weeks of pervasive low mood, low self-esteem, and loss of interest or pleasure in normally enjoyable activities. https://en.wikipedia.org/wiki/Major_depressive_disorder 严重抑郁症 Jian Guan (关健) 2025-03-23T02:09:08Z severe depression Major depressive disorder PICO:0000035 Data safety is protect the data that relating to occupational safety and health for the use of various substances and products. 数据安全 Jian Guan (关健) 2025-03-23T02:21:38Z data safety PICO:0000036 A process of identification of individual identity directly by technologies, or processes that those can re-identify the person indirectly through combination or other ways,including data obtained from multiple sources, or different media. https://en.wikipedia.org/wiki/Data_re-identification 重新识别 Jian Guan (关健) 2025-03-23T02:29:30Z re-identification de-anonymization PICO:0000037 The risk in data re-identification. 重新识别风险 Jian Guan (关健) 2025-03-23T02:32:33Z re-identification risk PICO:0000038 A kind of hypothetical "person" intended to re-identify the data risk determination. Assuming the person who knows of all the general technical knowledge of the related technical field, and is capable of knowing all the existing technology in the field, and has the ability to solve the general technical problems with conventional experimental means in the field. 一般技术人员 Jian Guan (关健) 2025-03-23T02:41:36Z general technician PICO:0000039 A frameworks, processes, and systems by which organizations, institutions, and governments are directed, controlled, and held accountable, through which guiding the organizations and governments through the challenges of decision-making while ensuring fairness, transparency, and accountability. 伦理治理 Jian Guan (关健) 2025-03-23T02:44:52Z ethics governance PICO:0000040 A part of management that deals with providing an ethical climate in organizations, both public and private, using specific tools such as ethical codes, ethical committees, ethical hotlines, whistleblowing procedures, ethical audit, and ethical trainings. 伦理管理 Jian Guan (关健) 2025-03-23T02:52:33Z ethical management PICO:0000041 Three fundamental ethical principles identified in the Belmont Report for all human subject research – respect for persons, beneficence, and justice, now is believed apply to all research and activities involving humans. 基本伦理原则 Jian Guan (关健) 2025-03-23T03:10:50Z basic ethical principle PICO:0000042 A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis. 伦理要求 Jian Guan (关健) 2025-03-23T05:23:25Z ethical requirement http://purl.obolibrary.org/obo/IAO_0000620 PICO:0000043 A practice of ehtical governance and management according to the research ethics. A data ethics review is the representative of practible ethics. 实践伦理学 Jian Guan (关健) 2025-03-23T05:27:20Z practible ethics PICO:0000044 A systematic evaluation process aimed at ensuring that research involving human participants is conducted in a manner that respects their rights, dignity, and welfare. This process often involves an ethics committee or institutional review board (IRB) that assesses the study's design, methodology, and potential risks to participants. Ethical reviews are crucial for maintaining the integrity of research and ensuring compliance with legal and ethical standards. 伦理审查 Jian Guan (关健) 2025-03-23T05:33:24Z ethical review PICO:0000045 A systematic evaluation process aimed at ensuring that research involving human participants is conducted in a manner that respects their rights, dignity, and welfare. 数据伦理审查 Jian Guan (关健) 2025-03-23T05:35:46Z data ethics review PICO:0000046 Research is creative and systematic work undertaken to increase the stock of knowledge. It involves the collection, organization, and analysis of evidence to increase understanding of a topic, characterized by a particular attentiveness to controlling sources of bias and error. These activities are characterized by accounting and controlling for biases. A research project may be an expansion of past work in the field. To test the validity of instruments, procedures, or experiments, research may replicate elements of prior projects or the project as a whole. https://en.wikipedia.org/wiki/Research 研究 Jian Guan (关健) 2025-03-23T05:43:35Z research http://purl.obolibrary.org/obo/GSSO_006620 PICO:0000047 Data driven research is a subset of the field of digital humanities that deals particularly with data analytic and visualization methodologies. This field broadly consists of theories and methodologies from a range of humanities disciplines that inform how a researcher gathers, analyzes, and filters datasets to gain insight about a particular subject. https://en.wikipedia.org/w/index.php?search=data-driven+research&title=Special%3ASearch&ns0=1 数据驱动研究 Jian Guan (关健) 2025-03-23T05:46:21Z data-driven research PICO:0000048 Algorithm-based data analysis activities. 涉及算法的数据活动 Jian Guan (关健) 2025-03-23T05:50:33Z data activity involving algorithms PICO:0000049 Processing of personal information data. 涉及个人信息的数据处理 Jian Guan (关健) 2025-03-23T05:57:41Z data processing involving personal information PICO:0000050 An ethical principle of guaranttee individual's rights and interests. Which incorporates at least two ethical convictions: first, that individuals should be treated as autonomous agents, and second, that persons with diminished autonomy are entitled to protection. Which divides into two separate moral requirements: the requirement to acknowledge autonomy and the requirement to protect those with diminished autonomy. Belmont Report 尊重原则 Jian Guan (关健) 2025-03-23T06:01:32Z respect for person PICO:0000051 The ethical obligations of GOVERNMENT with particular attention to related institutes and individuals of high risk research and activities, and their ethical research and ethical review competence, and assessment of ethical review decisions, ethical training, etc. 伦理监管 Jian Guan (关健) 2025-03-23T06:04:54Z ethical supervision PICO:0000052 The principle that a person should have control over their personal data, including the ability to decide how organizations collect, store and use their data. 数据隐私 Jian Guan (关健) 2025-03-23T06:18:17Z data privacy information privacy PICO:0000053 A legislative concept, and one of the ethical requirement of 'Beneficence' ethical principle application in research practice and data activities involving humans for ethical acceptance. 隐私保护 Jian Guan (关健) 2025-03-23T06:19:49Z privacy protection PICO:0000054 ‌1. Oral notification: applicable to general drug treatment, routine clinical examination and other situations, as well as emergency or need timely change of the situation and emergency rescue measures. After the event, the medical staff shall keep faithful and detailed records as medical certification materials. ‌2. Written notification form: this is the principle form, such as surgery notice, blood transfusion notice, etc. The patient is required to understand and agree and sign. 传统知情同意模式 Jian Guan (关健) 2025-03-23T06:25:29Z traditional consent model PICO:0000055 泛知情同意，分层同意模式 Jian Guan (关健) 2025-03-23T06:30:35Z broad, tiered consent model PICO:0000056 泛知情同意，定期同意模式 Jian Guan (关健) 2025-03-23T06:32:05Z broad, periodic consent model PICO:0000057 泛知情同意，一次性同意模式 Jian Guan (关健) 2025-03-23T06:33:05Z broad, one time consent PICO:0000058 选择性退出 Jian Guan (关健) 2025-03-23T06:33:45Z opt-out consent model PICO:0000059 Active ablility is an ability to maintain mormal activity behavior. 行为能力 Jian Guan (关健) 2025-03-23T06:47:39Z active ability PICO:0000060 1. Those who are vulnerable or discriminated against because of their age, sex, physical condition, economic status, social status, etc. 2. Refers to the social, economic, cultural and other disadvantaged groups, such as the poor, disabled, ethnic minorities, etc. 弱势群体 Jian Guan (关健) 2025-03-23T06:51:34Z vulnerable group disadvantaged group PICO:0000061 诱导同意 Jian Guan (关健) 2025-03-23T06:59:57Z induced consent PICO:0000062 强迫同意 Jian Guan (关健) 2025-03-23T07:00:52Z forced consent PICO:0000063 The assessment of risks and benefits based on a careful arrayal of relevant data, including, in some cases, alternative ways of obtaining the benefits sought in the research and data activities. 风险和收益评估 Jian Guan (关健) 2025-03-23T07:03:31Z assessment of risks and benefits PICO:0000064 A resolution of action to be taken in an emergency to protect people's lives and property. 应急方案 Jian Guan (关健) 2025-03-23T07:14:22Z emergency resolution PICO:0000065 Beneficence is a concept in research ethics that states that researchers should have the welfare of the research participant as a goal of any clinical trial or other research study. The antonym of this term, maleficence, describes a practice that opposes the welfare of any research participant. According to the Belmont Report, researchers are required to follow two moral requirements in line with the principle of beneficence: do not harm and maximize possible benefits for research while minimizing any potential harm on others. https://en.wikipedia.org/wiki/Beneficence_(ethics) 有益原则 Jian Guan (关健) 2025-03-23T07:25:18Z beneficence PROCO:0000003 All information that has been made available to the public in any form before a given date that might be relevant to a patent's claims of originality. [wikipedia] prior art T4FS:0000012 A specific deed, action, function or sphere of action in relation with the role of data stewardship Yann Le Franc https://orcid.org/0000-0002-7702-4495 https://orcid.org/0000-0003-2687-1982 Set of actions carried out during data stewardship processes data stewardship activity T4FS:0000021 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. https://orcid.org/0000-0002-7702-4495 https://orcid.org/0000-0003-2687-1982 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. exposing data T4FS:0000025 Object, event or phenomenon about which data are stored in a database and which has intermediate representation in a Data Model. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0003-2687-1982 data entity T4FS:0000032 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. The standard user and application program interface to a relational database is the structured query language (SQL). https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0002-7702-4495 https://orcid.org/0000-0003-2687-1982 relational database T4FS:0000036 Managing and promoting the use of assets from their point of creation to ensure that they are fit for contemporary purpose and available for discovery and reuse. For dynamic datasets this may mean continuous enrichment or updating to keep them fit for purpose. Higher levels of curation will also involve links with annotation and with other published materials. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0003-2687-1982 curation T4FS:0000072 Collection of datasets sharing the same product specification. A dataset series is a type of aggregation or collection with some “logical grouping” such as by a topic (specification) with the (product) unit being a dataset series. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0003-2687-1982 dataset series T4FS:0000127 The World Wide Web Consortium’s Platform for Personal Privacy Project (P3P) offers specific recommendations for practices that will let users define and share personal information with Web sites that they agree to share it with. The P3P incorporates a number of industry proposals, including the Open Profiling Standard (OPS). Using software that adheres to the P3P recommendations, users will be able to create a personal profile, all or parts of which can be made accessible to a Web site as the user directs. A tool that will help a user decide whether to trust a given website with personal information is a Statement of Privacy Policy that a website can post. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0002-7702-4495 https://orcid.org/0000-0003-2687-1982 personal information privacy T4FS:0000141 The activities of data policies, data planning, data element standardization, information management control, data synchronization, data sharing, and database development, including practices and projects that acquire, control, protect, deliver and enhance the value of data and information. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0003-2687-1982 data management T4FS:0000213 Entire period of time that research data exists. This lifecycle describes the flow of research data starting from planning, collecting, processing, analysing, preserving, sharing and finally reusing the research data. Research data often have a longer lifespan than the research project. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0003-2687-1982 data lifecycle research data lifecycle T4FS:0000215 Repository for persistently storing collections of data, such as a database, a file system or a directory. The data stored can be of any type that can be rendered in digital format and placed in electronic media. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0003-2687-1982 data store T4FS:0000222 Data that relate to a living individual who can be identified from those data or those data plus other information which is in the possession of, or is likely to come into the possession of, the data controller, and includes any expression of opinion about the individual and any indication of the intentions of the data controller or any other person in respect of the individual. Any information that can be used to distinguish one person from another and can be used for de-anonymising anonymous data can be considered personally identifiable data. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0002-7702-4495 https://orcid.org/0000-0003-2687-1982 Personal data personally identifiable information T4FS:0000251 Voluminous amount of structured, semi-structured and/or unstructured data that have the potential to be mined for information, primarily characterised by big volume, extensive variety, high velocity (creation and use), and/or variability that together require a scalable architecture for efficient data storage, manipulation, and analysis. The definition is evolving and can vary by sector, depending on what kind of software tools are commonly available and what sizes of datasets are common in a particular discipline. With those caveats, big data in many sectors today will range from a few dozen terabytes to multiple petabytes. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0003-2687-1982 big data T4FS:0000347 Organised collection of data or objects in a computational format, that are generated or collected by researchers in the course of their investigations, regardless of their form or method, that form the object on which researchers test a hypothesis. This includes the full range of data: raw, unprocessed datasets, proprietary generated and processed data and secondary data obtained from third parties. The presentation of the data in the application is enabled through metadata. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0003-2687-1982 dataset T4FS:0000352 Techniques that produce synthesised knowledge from organised information. Process of inspecting, cleaning, transforming, and modelling data with the goal of highlighting useful information suggesting conclusions, and supporting decision making. Data analysis has multiple facets and approaches, encompassing diverse techniques under a variety of names, in different business, science, and social science domains. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0003-2687-1982 data analysis T4FS:0000353 Resource management is the efficient and effective development of an organization's resources when they are needed. Such resources may include the financial resources, inventory, human skills, production resources, or information technology (IT) and natural resources. Kristina Hettne Leighton Christiansen Simon Hodson Victoria Dominguez Del Angel resource management T4FS:0000372 https://orcid.org/0000-0002-7702-4495 https://orcid.org/0000-0003-2687-1982 data stewardship technical concept T4FS:0000397 Collection of data that is organised according to a conceptual structure/model describing the characteristics of these data and the relationships among their corresponding entities, supporting one or more application areas. A database allows its contents to be easily accessed, managed and updated. The type of database used depends on the requirements of the study. A common type is the relational database, where data are related to each other in a systematic manner so that they can be reorganised and accessed in a number of different ways. A database may house one or many datasets. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0003-2687-1982 database T4FS:0000430 Facts, measurements, recordings, records, or observations about the world, collected by researchers, that are yet to be processed/interpreted/analysed. Data may be in any format or medium taking the form of writings, notes, numbers, symbols, text, images, films, video, sound recordings, pictorial reproductions, drawings, designs or other graphical representations, procedural manuals, forms, diagrams, work flow charts, equipment descriptions, data files, data processing algorithms, or statistical records. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0003-2687-1982 data T4FS:0000458 Exercise of authority, control and shared decision making (planning, monitoring and enforcement) over the management of data assets. Overall management of the availability, usability, integrity, and security of the data employed in an organisation. A sound data governance program includes a governing body or council, a defined set of procedures, and a plan to execute those procedures. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0003-2687-1982 data governance T4FS:0000472 1. Exercising authority to provide direction and to undertake, coordinate, and regulate activities in support of achieving this direction and desired outcomes. Governance can be thought of as the role of an organization's board of directors or its equivalent that is focused on defining that organization's purpose and the development of the strategies, objectives, values, and policies that frame how that purpose will be pursued. It includes the development of such things as mission statements, statements of organizational objectives and values, logic models, organizational performance metrics, risk management frameworks, policies and guidelines for financial and operational matters, stakeholder relations, etc. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0003-2687-1982 governance T4FS:0000482 Practice of making data available for checking, reproducing or reusing. The mechanisms available for achieving this are: making data available on request, as supplementary information to journal articles, or as published datasets in data repositories. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0002-7702-4495 https://orcid.org/0000-0003-2687-1982 Data dissemination Data posting data sharing T4FS:0000487 Combining diverse datasets from disparate sources into one unified dataset or database. Data are accessed and extracted, moved, validated, cleaned, transformed and loaded. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0002-7702-4495 https://orcid.org/0000-0003-2687-1982 data integration T4FS:0000518 Data that are used as primary sources to support technical or scientific enquiry, research, scholarship, or artistic activity, and that are used as evidence in the research process and/or are commonly accepted in the research community as necessary to validate research findings and results. All other digital and non-digital content have the potential of becoming research data. Research data may be experimental data, observational data, operational data, third party data, public sector data, monitoring data, processed data, or repurposed data. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0002-7702-4495 https://orcid.org/0000-0003-2687-1982 research data T4FS:0000533 Analysing multivariate datasets using pattern recognition or other knowledge discovery techniques to identify potentially unknown and potentially meaningful data content, relationships, classification or trends. Data mining parameters include: Association (looking for patterns where one event is connected to another event); Sequence or path analysis (looking for patterns where one event leads to another later event); Classification (looking for new patterns); Clustering (finding and visually documenting groups of facts not previously known); Forecasting, or predictive analytics (discovering patterns in data that can lead to reasonable predictions about the future. https://orcid.org/0000-0002-5214-4466 https://orcid.org/0000-0003-2687-1982 data mining TXPO:0000300 This is an abstraction of the kinds at the class level. In the use case, it is sometimes referred to with # operator as a class constraint like "#generic quality". In a common term, it would be called "attribute". Its instance is not equal to its value. The value itself belongs to "quality value". Its instance is still an attribute which refers to a specific quantity. Its instnace plays a quality role like length plays one's height as a quality role. Quality such as one's height, one's weight, etc. are roles, and hence must be defined in the context of respective contexts(entities). Therefore, they are not defined as basic type like length, weight, etc. See "physical" in which a most generic quality is defined. Quality in DOLCE corresponds to quality role type in YAMATO. This is why "quality" is invisible in YAMATO in spite of it knows "quality". YAMATO Ontology generic quality attribute resource:SIO_000078 SIO_000078 A language entity implements some language specification for the visual interpretation and is part of some document. nlp+ language entity resource:SIO_000088 SIO_000088 A record is a document containing a collection of statements about some entity. record resource:SIO_000136 SIO_000136 A description is language entity in which elements of a language (formal or natural) are used to characterize an entity. description resource:SIO_000256 SIO_000256 A proposition is a sentence expressing something true or false. proposition resource:SIO_000472 SIO_000472 scientific data is data obtained from some scientific procedure. scientific data resource:SIO_000999 SIO_000999 A procedure is a process that attempts to achieve one or more objectives by following an established set of actions. procedure resource:SIO_001183 SIO_001183 A statement is a proposition that is either (a) a meaningful declarative sentence that is either true or false, or (b) that which a true or false declarative sentence asserts. statement resource:SIO_001330 SIO_001330 metadata is data that provides information about data. metadata resource:SIO_010019 SIO_010019 biological data is scientific data relevant to biology. biological data resource:SIO_010298 SIO_010298 medical data is data of interest to medicine. medical data The storing of digital information. Often this is done for archiving and retrieval purposes. data storage owl:Thing example to be eventually removed metadata complete organizational term ready for release metadata incomplete uncurated pending final vetting to be replaced with external ontology term requires discussion Glossary (Anti-Racism Digital Library) Encyclopedia of Homosexuality The Wiley Blackwell Encyclopedia of Gender and Sexuality Studies Glossary of HIV/AIDS-Related Terms BDSM And Kink Terminology: A To Z Global Encyclopedia of Lesbian, Gay, Bisexual, Transgender, and Queer (LGBTQ) History LGBTQ America Today: An Encyclopedia Encyclopedia of Lesbian, Gay, Bisexual and Transgender History in America 1.0.0 BFO 2 Reference: BFO does not claim to provide complete coverage of entities of all types. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning - coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation. BFO 2 Reference: BFO's treatment of continuants and occurrents - as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality - earlier called the 'SNAP' and 'SPAN' perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science. BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. 'Entity' is an example of a primitive term. Primitive terms in a highest-level ontology such as BFO are terms that 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. Alan Ruttenberg Albert Goldfain Barry Smith Bill Duncan Bjoern Peters Chris Mungall David Osumi-Sutherland Fabian Neuhaus Holger Stenzhorn James A. Overton Janna Hastings Jie Zheng Jonathan Bona Larry Hunter Leonard Jacuzzo Ludger Jansen Mark Ressler Mathias Brochhausen Mauricio Almeida Melanie Courtot Pierre Grenon Randall Dipert Ron Rudnicki Selja Seppälä Stefan Schulz Thomas Bittner Werner Ceusters Yongqun "Oliver" He Jian Guan (关健) Jiangan Xie (谢江安) 2025-01-18 The Pathogen-related Informed Consent Ontology (PICO) is an ontology for the informed consent and informed consent process in the pathogen-related medical fields, especially for pathological data use. Pathogen-related Informed Consent Ontology (PICO：病原体相关知情同意本体) http://creativecommons.org/licenses/by/4.0/ PICO is an application ontology for the standardization of pathogen-related informed consent data and the classification of term logical relations. The current focus of PICO development is to represent different pathogenetic data use in such a way that it will support consistent representation of medical questionnaires. Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif. The BSD license on the BFO project site refers to code used to build BFO. This BFO 2.0 version represents a major update to BFO and is not strictly backwards compatible with BFO 1.1. The previous OWL version of BFO, version 1.1.1 will remain available at http://ifomis.org/bfo/1.1 and will no longer be updated. The BFO 2.0 OWL is a classes-only specification. The incorporation of core relations has been held over for a later version. https://github.com/PICO-ontology/PICO 1.0.0 2012-06-14 Dublin Core Metadata Element Set, Version 1.1 Spatial topic and spatial applicability may be a named place or a location specified by its geographic coordinates. Temporal topic may be a named period, date, or date range. A jurisdiction may be a named administrative entity or a geographic place to which the resource applies. Recommended practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names [[TGN](https://www.getty.edu/research/tools/vocabulary/tgn/index.html)]. Where appropriate, named places or time periods may be used in preference to numeric identifiers such as sets of coordinates or date ranges. 1999-07-02 The spatial or temporal topic of the resource, spatial applicability of the resource, or jurisdiction under which the resource is relevant. Coverage A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/coverage) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation. Recommended practice is to use a controlled vocabulary where available. For example, for file formats one could use the list of Internet Media Types [[MIME](https://www.iana.org/assignments/media-types/media-types.xhtml)]. 1999-07-02 The file format, physical medium, or dimensions of the resource. Format A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/format) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation. Recommended practice is to use either a non-literal value representing a language from a controlled vocabulary such as ISO 639-2 or ISO 639-3, or a literal value consisting of an IETF Best Current Practice 47 [[IETF-BCP47](https://tools.ietf.org/html/bcp47)] language tag. 1999-07-02 A language of the resource. Language A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/language) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation. Examples of a Publisher include a person, an organization, or a service. Typically, the name of a Publisher should be used to indicate the entity. 1999-07-02 An entity responsible for making the resource available. Publisher A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/publisher) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation. Typically, rights information includes a statement about various property rights associated with the resource, including intellectual property rights. 1999-07-02 Information about rights held in and over the resource. Rights A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/rights) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation. The described resource may be derived from the related resource in whole or in part. Recommended best practice is to identify the related resource by means of a string conforming to a formal identification system. 1999-07-02 A related resource from which the described resource is derived. Source A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/source) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation. Typically, the subject will be represented using keywords, key phrases, or classification codes. Recommended best practice is to use a controlled vocabulary. 1999-07-02 The topic of the resource. Subject A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/subject) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation. Recommended practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [[DCMI-TYPE](http://dublincore.org/documents/dcmi-type-vocabulary/)]. To describe the file format, physical medium, or dimensions of the resource, use the Format element. 1999-07-02 The nature or genre of the resource. Type A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/type) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.