Asiyah Yu Lin (CDRH, Food and Drug Administration) Astghik Sargsyan (Fraunhofer SCAI) Geena Mariya Jose (Causality Biomodels) Leon Li (NIH) Oliver He (University of Michigan) Shounak Baksi (Causality Biomodels) The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials. Alpha Tom Kodamullil (Fraunhofer SCAI) Johannes Darms (Fraunhofer SCAI) Stephan Gebel (Fraunhofer SCAI) Sumit Madan (Fraunhofer SCAI) http://creativecommons.org/licenses/by/4.0 CTO: Core Ontology of Clinical Trials Version Release: 1.0.0 BFO OWL specification label Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label BFO OWL specification label BFO CLIF specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label BFO CLIF specification label editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example example of usage A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status definition definition textual definition 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. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> DEFINITION definition definition textual definition 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> 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> definition editor definition editor term editor term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term alternative term definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source 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 elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) has associated axiom(fol) has axiom label A property created to allow the source NICHD to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are the contributing source. An association created to allow the source NICHD to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are a contributing source. A11 Conceptual Entity Has_NICHD_Parent Has_NICHD_Parent Has_NICHD_Parent true A property representing a concept unique identifier within the NCI Enterprise Vocabulary Service's NCI Thesaurus. NHC0 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. The semantic type describes 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. Provides 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. 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. Concept Unique Identifiers, or CUIs, are concept numbers 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 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. This 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. English language definitions of what a source other than NCI means by the concept. These are limited to 1024 characters. They include information about the definition's source in a form that can easily be interpreted by software. 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. 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 A property representing a term chosen by NICHD to be used in the representation of the NICHD hierarchy. P371 Conceptual Entity NICHD_Hierarchy_Term NICHD NICHD_Hierarchy_Term NICHD_Hierarchy_Term 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. Design notes are 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 NIAID GSCID-BRC alternative term An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC alternative term IEDB alternative term An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term An annotation property that refers to a code defined by NCIT NCIT code A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy has_rank Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Description The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Source has_alternative_id database_cross_reference 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. 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. FULL_SYN Synonym with Source Data has exact synonym has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym An association that connects the concept defining a particular terminology subset with concepts that belong to this subset. Used to associate the concept defining a particular terminology subset with concepts that belong to this subset. Concept_In_Subset in subset in_subset shorthand label label label has part realizes preceded by preceded_by is about has_specified_input has participant concretizes has role entity 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]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant (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] 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] 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] 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] 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] 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] 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] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] 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] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable 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] 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] 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] 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] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] 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] 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] 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] 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] 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] 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]) gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] 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] 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] 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] material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity 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] 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] 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 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] 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] 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] 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] 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] 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] 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]) molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well molecular entity chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chebi_ontology CHEBI:24431 chemical entity An identifier(s) (ID), if any, other than the organization's Unique Protocol Identification Number or the NCT number that is assigned to the clinical study. This includes any unique clinical study identifiers assigned by other publicly available clinical trial registries. If the clinical study is funded in whole or in part by a U.S. Federal Government agency, the complete grant or contract number must be submitted as a Secondary ID. Other identifiers besides the Trial Identifying Number allocated by the Primary Registry, if any. secondary identifier An identifier(s) (ID), if any, other than the organization's Unique Protocol Identification Number or the NCT number that is assigned to the clinical study. This includes any unique clinical study identifiers assigned by other publicly available clinical trial registries. If the clinical study is funded in whole or in part by a U.S. Federal Government agency, the complete grant or contract number must be submitted as a Secondary ID. https://prsinfo.clinicaltrials.gov/definitions.html Other identifiers besides the Trial Identifying Number allocated by the Primary Registry, if any. https://www.who.int/ictrp/network/trds/en/ A centrally registered identifier that is assigned for a specific clinical trial registered in the Australian New Zealand clinical trials registry (ANZCTR). The format for the registry number is “ACTRN” followed by a 14-digit number, e.g., ACTRN12620000457943. ANZCTR identifier Australian New Zealand clinical trials registry identifier http://www.anzctr.org.au/ https://www.who.int/ictrp/network/primary/en/ Australian New Zealand Clinical Trials Registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. ANZCTR Australian New Zealand clinical trials registry http://www.anzctr.org.au/ https://www.who.int/ictrp/network/primary/en/ A centrally registered identifier that is assigned for a specific clinical trial registered in the Peruvian clinical trial registry (REPEC). The format for the registry number is “PER-” followed by a 3-digit number, followed by a hyphen, followed by a 2-digit number e.g., PER-010-20. REPEC identifier Peruvian clinical trial registry identifier https://ensayosclinicos-repec.ins.gob.pe/en/ https://www.who.int/ictrp/network/primary/en/ The party or parties involved in the clinical trial who are prevented from having knowledge of the interventions assigned to individual participants. blinding masking masking design http://www.icmje.org/recommendations/ http://www.who.int/ictrp/network/trds/en/index.html The party or parties involved in the clinical trial who are prevented from having knowledge of the interventions assigned to individual participants. https://prsinfo.clinicaltrials.gov/definitions.html Participants are expressly assigned to intervention groups through a non-random method, such as physician choice non-randomized nonrandomized non-random allocation Participants are expressly assigned to intervention groups through a non-random method, such as physician choice https://prsinfo.clinicaltrials.gov/definitions.html A study record that includes the summary results posted in the ClinicalTrials.gov results database. Summary results information includes participant flow, baseline characteristics, outcome measures, and adverse events (including serious adverse events). summary results study summary result https://www.who.int/ictrp/network/trds/en/ A study record that includes the summary results posted in the ClinicalTrials.gov results database. Summary results information includes participant flow, baseline characteristics, outcome measures, and adverse events (including serious adverse events). https://clinicaltrials.gov/ct2/about-studies/glossary A description of each secondary outcome measure (or for observational studies, specific secondary measurement[s] or observation[s] used to describe patterns of diseases or traits or associations with exposures, risk factors or treatment). Each secondary outcome measure information includes title, description and time frame. https://prsinfo.clinicaltrials.gov/definitions.html key secondary outcome secondary outcome measure information https://clinicaltrials.gov/ct2/about-studies/glossary key secondary outcome https://www.who.int/ictrp/network/trds/en/ The Iranian registry of clinical trials is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. IRCT Iranian registry of clinical trials http://www.irct.ir/ https://www.who.int/ictrp/network/primary/en/ Any other measurements, excluding post-hoc measures, that will be used to evaluate the intervention(s) or, for observational studies, that are a focus of the study. Each primary outcome measure information includes title, description and time frame. https://prsinfo.clinicaltrials.gov/definitions.html other pre-specified outcome measures other outcome measure information The Indian clinical trials registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. CTRI clinical trials registry - India Indian clinical trials registry http://ctri.nic.in/ https://www.who.int/ictrp/network/primary/en/ The Netherlands national trial register is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. NTR The Netherlands national trial register http://www.trialregister.nl/ https://www.who.int/ictrp/network/primary/en/ A centrally registered identifier that is assigned for a specific clinical trial registered in the Iranian registry of clinical trials (IRCT). The format for the registry number is “IRCT” followed by a 14-digit number, one letter and again one or two numbers, e.g., IRCT20100228003449N29. IRCT identifier Iranian registry of clinical trials identifier http://www.irct.ir/ https://www.who.int/ictrp/network/primary/en/ A centrally registered identifier that is assigned for a specific clinical trial registered in the German clinical trials register (DRKS). The format for the registry number is “DRKS” followed by a 8-digit number, e.g., DRKS00000494. DRKS identifier German clinical trials register identifier https://www.drks.de/drks_web/ https://www.who.int/ictrp/network/primary/en/ The Cuban public registry of clinical trials is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. RPCEC Cuban public registry of clinical trials http://registroclinico.sld.cu/en/home https://www.who.int/ictrp/network/primary/en/ For clinical trials, a planned measurement described in the protocol that is used to determine the effect of an intervention/treatment on participants. For observational studies, a measurement or observation that is used to describe patterns of diseases or traits, or associations with exposures, risk factors, or treatment. Types of outcome measures include primary outcome measure and secondary outcome measure. outcome measure outcome measurement clinical trial outcome measurement For clinical trials, a planned measurement described in the protocol that is used to determine the effect of an intervention/treatment on participants. For observational studies, a measurement or observation that is used to describe patterns of diseases or traits, or associations with exposures, risk factors, or treatment. Types of outcome measures include primary outcome measure and secondary outcome measure. https://clinicaltrials.gov/ct2/about-studies/glossary The Pan African clinical trial registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. PACTR Pan African clinical trial registry http://www.pactr.org/ https://www.who.int/ictrp/network/primary/en/ A centrally registered identifier that is assigned for a specific clinical trial registered in the The Netherlands national trial register (NTR). The format for the registry number is “NTR” followed by a 1 to 4-digit number, e.g., NL8498. NTR identifier The Netherlands national trial register identifier https://www.trialregister.nl/ https://www.who.int/ictrp/network/primary/en/ The JAPIC (Japan Pharmaceutical Information Center) clinical trials registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. JapicCTI JAPIC clinical trials registry https://rctportal.niph.go.jp/en/ https://www.japic.or.jp/ https://www.who.int/ictrp/network/primary/en/ A centrally registered identifier that is assigned for a specific clinical trial registered in the Pan African clinical trial register. The format for the registry number is “KCT” followed by a 15-digit number, e.g., PACTR202004893013257. PACTR identifier Pan African clinical trial registry identifier https://pactr.samrc.ac.za/ https://www.who.int/ictrp/network/primary/en/ A centrally registered identifier that is assigned for a specific clinical trial registered in the Chinese clinical trials register (ChiCTR). The format for the registry number is “ChiCTR” followed by a 10-digit number, e.g., ChiCTR2000031589. ChiCTR identifier Chinese Clinical Trial Register number Chinese clinical trail registry identifier http://www.chictr.org.cn/enIndex.aspx The Lebanese clinical trials registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. LBCTR Lebanese clinical trials registry http://lbctr.emro.who.int/ https://www.who.int/ictrp/network/primary/en/ German clinical trials register is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. DRKS German clinical trials register http://www.germanctr.de/ https://www.who.int/ictrp/network/primary/en/ The JMACCT (Japan Medical Association, Center for Clinical Trials) clinical trials registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. JMACCT JMACCT clinical trials registry https://dbcentre3.jmacct.med.or.jp/jmactr/Default_Eng.aspx https://rctportal.niph.go.jp/en/ adult (18-64) age_between_18_and_64 https://clinicaltrials.gov/ct2/about-studies/glossary The actual total number of participants that are enrolled in a clinical study https://prsinfo.clinicaltrials.gov/definitions.html enrollment sample size number of participants http://www.icmje.org/recommendations/ enrollment https://prsinfo.clinicaltrials.gov/definitions.html sample size http://www.who.int/ictrp/network/trds/en/index.html A centrally registered identifier that is assigned for a specific clinical trial registered in Brazilian Registry of Clinical Trials (ReBEC). The format for the ReBEC registry number is “RBR-” followed by 6 characters, e.g., RBR-4hb9qs. Brazilian Registry of Clinical Trials identifier ReBEC identifier Brazilian clinical trial registry identifier http://www.ensaiosclinicos.gov.br/ Clinical trial phase that is a combination of phases 2 and 3. Phase 2/3 Phase 2/Phase 3 Phase I/II clinical trial phase 2/3 https://prsinfo.clinicaltrials.gov/definitions.html data item .... study result A type of eligibility criteria that indicates whether people who do not have the condition/disease being studied can participate in that clinical study. Indication that participants who do not have a disease or condition, or related conditions or symptoms, under study in the clinical study are permitted to participate in the clinical study. accepts healthy volunteers healthy volunteer criterion https://www.who.int/ictrp/network/trds/en/ A type of eligibility criteria that indicates whether people who do not have the condition/disease being studied can participate in that clinical study. https://clinicaltrials.gov/ct2/about-studies/glossary Indication that participants who do not have a disease or condition, or related conditions or symptoms, under study in the clinical study are permitted to participate in the clinical study. https://prsinfo.clinicaltrials.gov/definitions.html child (birth-17) age_between_birth_and_17_years A description of each primary outcome measure (or for observational studies, specific key measurement[s] or observation[s] used to describe patterns of diseases or traits or associations with exposures, risk factors or treatment). Each primary outcome measure information includes title, description and time frame. https://prsinfo.clinicaltrials.gov/definitions.html primary end point primary outcome(s) primary outcome measure information https://clinicaltrials.gov/ct2/about-studies/glossary primary end point https://www.clinicaltrialsregister.eu/doc/EU_Clinical_Trials_Register_Glossary.pdf primary outcome(s) https://www.who.int/ictrp/network/trds/en/ The EU clinical trials register is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. EU-CTR EU clinical trials register https://eudract.ema.europa.eu/ https://www.clinicaltrialsregister.eu https://www.who.int/ictrp/network/primary/en/ The UMIN (University Hospital Medical Information Network Center) clinical trials registry is a Japanese primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. UMIN CTR UMIN clinical trials registry https://rctportal.niph.go.jp/en/ https://www.umin.ac.jp/ctr/ https://www.who.int/ictrp/network/primary/en/ older adult (65+) age_older_than_64 https://clinicaltrials.gov/ct2/about-studies/glossary Data generated from measurement of experimental variables in a study, or for observational studies, from descriptions of patterns of diseases or traits or associations with exposures, risk factors or treatment. outcome measure result Indicate whether a clinical study has been reviewed and approved by at least one human subjects protection review board or such review is not required per applicable law (for example, 21 CFR Part 56, 45 CFR Part 46, or other applicable regulation). human subjects protection review board status Indicate whether a clinical study has been reviewed and approved by at least one human subjects protection review board or such review is not required per applicable law (for example, 21 CFR Part 56, 45 CFR Part 46, or other applicable regulation). https://prsinfo.clinicaltrials.gov/definitions.html ClinicalTrials.gov is a registry of clinical trials. The Korean clinical trials registry (Clinical Research Information Service (CRiS), Republic of Korea) is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. CRiS Clinical Research Information Service, Republic of Korea Korean clinical trials registry http://cris.nih.go.kr/cris/en/use_guide/cris_introduce.jsp https://www.who.int/ictrp/network/primary/en/ Trials without phases (for example, studies of devices or behavioral interventions). N/A phase not applicable Trials without phases (for example, studies of devices or behavioral interventions). https://prsinfo.clinicaltrials.gov/definitions.html Look back using observations collected predominantly prior to subject selection and enrollment retrospective study design Look back using observations collected predominantly prior to subject selection and enrollment https://prsinfo.clinicaltrials.gov/definitions.html A centrally registered identifier that is assigned for a specific clinical trial registered in the international standard randomised controlled trial register (ISRCT). The format for the registry number is “ISRCTN” followed by a 8-digit number, e.g., ISRCTN14966673. ISRCTN International Standard Randomised Controlled Trial Number International standard randomised controlled trial register identifier http://www.isrctn.com/ https://www.who.int/ictrp/network/primary/en/ Clinical trial phase that is a combination of phases 1 and 2. Phase 1/2 Phase 1/Phase 2 Phase I/II clinical trial phase 1/2 https://prsinfo.clinicaltrials.gov/definitions.html Look forward using periodic observations collected predominantly following subject enrollment prospective study design Look forward using periodic observations collected predominantly following subject enrollment https://prsinfo.clinicaltrials.gov/definitions.html A centrally registered identifier that is assigned for a specific clinical trial registered in the Thai clinical trials registry (TCTR). The format for the registry number is “TCTR” followed by a 11-digit number, e.g., TCTR20200405001 TCTR identifier Thai clinical trials registry identifier http://www.clinicaltrials.in.th/ https://www.who.int/ictrp/network/primary/en/ The Chinese clinical trial registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. ChiCTR Chinese clinical trial registry http://www.chictr.org.cn/ https://www.who.int/ictrp/network/primary/en/ The Thai clinical trials registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. TCTR Thai clinical trials registry http://www.clinicaltrials.in.th/ https://www.who.int/ictrp/network/primary/en/ A description of the outcome measure in an interventional study or for observational studies, specific key measurement[s] or observation[s] used to describe patterns of diseases or traits or associations with exposures, risk factors or treatment. outcome specification https://clinicaltrials.gov/ct2/about-studies/glossary A centrally registered identifier that is assigned for a specific clinical trial registered in the Indian clinical trial register. The format for the registry number is “CRTI/” followed by a 4-digit number, followed by a slash, followed a 2-digit number, followed by a slash, followed a 6-digit number, e.g., CTRI/2020/03/024402. CRTI identifier Clinical Trials Registry - India identifier Indian clinical trial registry identifier http://ctri.nic.in/Clinicaltrials/login.php https://www.who.int/ictrp/network/primary/en/ The Brazilian clinical trials registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. ReBec Brazilian clinical trials registry http://www.ensaiosclinicos.gov.br/ https://www.who.int/ictrp/network/primary/en/ A centrally registered identifier that is assigned for a specific clinical trial registered in the Japan Registry of Clinical Trials (jRCT). The format for the registry number is “jRCTs” followed by a 9-digit number, e.g., JPRN-jRCTs031190227 Japan registry of clinical trials identifier jRCT clinical trial identifier https://jrct.niph.go.jp/ https://rctportal.niph.go.jp/en/ https://www.who.int/ictrp/network/primary/en/ A centrally registered identifier that is assigned for a specific clinical trial registered in the Cuban public registry of clinical trials (RPCEC). The format for the registry number is “RPCEC” followed by a 8-digit number, e.g., RPCEC00000306. RPCEC identifier Cuban public registry of clinical trials identifier http://registroclinico.sld.cu/en/home https://www.who.int/ictrp/network/primary/en/ A centrally registered identifier that is assigned for a specific clinical trial registered in the Lebanese clinical trials registry (LBCTR). The format for the registry number is “LBCTR” followed by a 10-digit number, e.g., LBCTR2020043459. Lebanese clinical trials registry identifier LBCTR identifier http://lbctr.emro.who.int/ https://www.who.int/ictrp/network/primary/en/ A primary registry is clinical trial registry in the WHO registry network that meet specific criteria for content, quality and validity, accessibility, unique identification, technical capacity and administration. Primary registries also meet the requirements of the International Clinical Trials Registry Platform (ICMJE). primary registry https://www.who.int/ictrp/network/primary/en/ The Peruvian clinical trial registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. REPEC Peruvian clinical trial registry https://ensayosclinicos-repec.ins.gob.pe/en/ https://www.who.int/ictrp/network/primary/en/ The Sri Lanka clinical trials registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. SLCTR Sri Lanka clinical trials registry http://www.slctr.lk/ https://www.who.int/ictrp/network/primary/en/ ClinicalTrials.gov is a registry for clinical trials. ClinicalTrials.gov ClinicalTrial.gov registry https://clinicaltrials.gov/ A clinical trials registry is a specifc registry type that enables the registration and documentation of clinical trials. clinical trials registry clinical trial enrollment clinical trial participant healthy enrollee enrolled patient placebo medical intervention outcome measurement datum primary outcome measurement datum secondary outcome measurement datum investigational molecular entity drug clinical trial clinical trial sponsor role procedure clinical trIal a study design in which neither the subjects nor the investigators are permitted to know which subject is receiving which treatment double-blind double-blinded double blinded design a study design in which only the investigators are permitted to know which subject is receiving which treatment double blind double blinded single blinded design a study design in which the subjects and the investigators are permitted to know which subject is receiving which treatment open blind open label open blinded design Groups of participants are assigned to receive interventions based on prior milestones being reached in the study, such as in some dose escalation and adaptive design studies sequential design Groups of participants are assigned to receive interventions based on prior milestones being reached in the study, such as in some dose escalation and adaptive design studies https://prsinfo.clinicaltrials.gov/definitions.html study design with a single group (arm) sinlge arm single arm design primary outcome measurement secondary outcome measurement a material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role William Hogan William Hogan drug product epidemiological study A study of the populations and demographic of the avian flu. A human study of diseases in populations of humans or other animals, specifically how, when and where they occur. Epidemiological studies can never prove causation, epidemiological evidence can only show that this risk factor is correlated with a higher incidence of disease in the population exposed to that risk factor. The higher the correlation the more certain the association, but it cannot prove the causation. PERSON: Karen Corday http://pmep.cce.cornell.edu/profiles/extoxnet/TIB/epidemiology.html epidemiological study A blood pressure monitor is a medical device. An instrument used in the diagnosis of disease or other conditions or for use in the care, treatment, or prevention of disease that does not achieve any of its primary intended purposes by chemical action or by being metabolized. PERSON: Nicole Vasilevsky http://medical-dictionary.thefreedictionary.com/medical+device medical device A preliminary study to determine the practicability of a proposed health program or procedure or of a larger study and to appraise the factors that may influence its practicability. A feasibility study aims to discover those things which may affect successful study conduct on a larger scale. PERSON: Melanie Wilson Dictionary of Epidemiology, 5th edition. feasibility study An organization dedicated to the collection, storage and dissemination of a set of scientific or clinical data. PERSON: Nicole Vasilevsky PERSON: Scott Hoffmann registry https://www.who.int/ictrp/network/trds/en/ objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take Alan Ruttenberg OBI Plan and Planned Process branch action specification data item Data items include counts of things, analyte concentrations, and statistical summaries. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item 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. An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity 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 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 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 report Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record) 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted. 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification PERSON: Alan Ruttenberg PERSON: Melanie Courtot PERSON:Chris Stoeckert GROUP: OBI OBI_0000099 report 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 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 that, when concretized, 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. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg 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 textual entity Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. PERSON: Lawrence Hunter text textual entity 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 A textual entity that is used as directive to deliver something to a person, or organization 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59 postal address email address Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583 Person:Alan Ruttenberg Person:Chris Stoeckart email address Entries in a Column of which the header is "Pubmed ID" PMID:12345 The following URL: "http://www.ncbi.nlm.nih.gov/pubmed/19918065" The following sentence contains a CRID: "The article with Pubmed ID: 19918065". The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs. 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Centrally Registered IDentifier Original proposal from Bjoern, discussions at IAO calls http://purl.obolibrary.org/obo/iao.owl Primary Registry and Trial Identifying Number CRID centrally registered identifier Primary Registry and Trial Identifying Number http://www.icmje.org/recommendations/ http://www.who.int/ictrp/network/trds/en/index.html Home institution of the contact person. value-type:xsd:string MS MS:1000590 contact affiliation GC_ID:1 ncbi_taxonomy all root GC_ID:1 ncbi_taxonomy biota cellular organisms GC_ID:1 PMID:23020233 PMID:30257078 eucaryotes eukaryotes ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes Eukaryota GC_ID:1 mammals ncbi_taxonomy mammals Mammalia GC_ID:1 Vertebrata vertebrates ncbi_taxonomy vertebrates Vertebrata <vertebrates> Homo sapiens Homo sapiens human human being man person GC_ID:1 human man ncbi_taxonomy Home sapiens Homo sampiens Homo sapeins Homo sapian Homo sapians Homo sapien Homo sapience Homo sapiense Homo sapients Homo sapines Homo spaiens Homo spiens Humo sapiens humans Homo sapiens Homo sapiens Records containing any interim or final results, as well as clinical and statistical descriptions, presentations, analyses and interpretations of any therapeutic, prophylactic, or diagnostic agent used in human subjects in a clinical trial. C115575 Intellectual Product Clinical Trial Final Report C3889645 CDISC-GLOSS CareLex A written description of a trial/study of any therapeutic, prophylactic, or diagnostic agent conducted in human subjects, in which the clinical and statistical description, presentations, and analyses are fully integrated into a single report. [ICH E3] Subcategory name for the eTMF domain used to classify clinical study report documents. CTrial Fin Rept Subcat Central Trial Final Reports Subcategory Clinical Trial Final Report Reports final report Clinical Trial Final Report An observational study that is also considered to be a Patient Registry. This type of study should only be registered once in the Protocol Registration and Results System (PRS), by the sponsor responsible for the primary data collection and analysis. Observational studies which include an organized system that uses observational methods to collect uniform data (clinical and other) prospectively for a population defined by a particular disorder/disease, condition (including susceptibility to a disorder), or exposure (including products, health care services, and/or procedures) and that serves a predetermined scientific, clinical, or policy purpose. Patient registries may be single purpose or on-going data collection programs that address one or more questions. (AHRQ) C129000 Research Activity Patient Registry Study C0920631 CDISC Observational studies which include an organized system that uses observational methods to collect uniform data (clinical and other) prospectively for a population defined by a particular disorder/disease, condition (including susceptibility to a disorder), or exposure (including products, health care services, and/or procedures) and that serves a predetermined scientific, clinical, or policy purpose. Patient registries may be single purpose or on-going data collection programs that address one or more questions. (AHRQ) PATIENT REGISTRY Patient Registry Study Patient Registry Study An observational study that is also considered to be a Patient Registry. This type of study should only be registered once in the Protocol Registration and Results System (PRS), by the sponsor responsible for the primary data collection and analysis. https://prsinfo.clinicaltrials.gov/definitions.html An intervention of a device product is being evaluated to determine the feasibility of the product or to test a prototype device and not health outcomes. Such studies are conducted to confirm the design and operating specifications of a device before beginning a full clinical trial. (ClinicalTrials.gov) C139174 Research Activity Device Feasibility Study CL526612 CDISC An intervention of a device product is being evaluated to determine the feasibility of the product or to test a prototype device and not health outcomes. Such studies are conducted to confirm the design and operating specifications of a device before beginning a full clinical trial. (ClinicalTrials.gov) DEVICE FEASIBILITY Device Feasibility Device Feasibility Study Device Feasibility Study The nature of the investigation or the investigational use for which clinical study is being done. C142175 Research Activity Study Type CL540168 CDISC Describes the role the study plays in determining the interventions a subject receives. STYPE Study Type Study Type https://prsinfo.clinicaltrials.gov/definitions.html https://www.who.int/ictrp/network/trds/en/ Participants are assigned to intervention groups by chance The process of resource distribution that is done by chance. C142660 Activity Random Allocation CL540611 CDISC-GLOSS Assignment of subjects to treatment (or control) groups in an unpredictable way. NOTE: in a blinded study, assignment sequences are concealed, but available for disclosure in the event a subject has an adverse experience. Random Allocation random allocation randomized Random Allocation Participants are assigned to intervention groups by chance https://prsinfo.clinicaltrials.gov/definitions.html The main objective of the intervention(s) being evaluated by the clinical trial. The principal reason or intention for the execution of an interventional or non-interventional clinical study. C147141 Idea or Concept Study Primary Purpose CL545057 CDISC The principal reason or intention for the execution of an interventional or non-interventional clinical study. (NCI) Study Primary Purpose Study Primary Purpose http://www.icmje.org/recommendations/ http://www.who.int/ictrp/network/trds/en/index.html The main objective of the intervention(s) being evaluated by the clinical trial. https://prsinfo.clinicaltrials.gov/definitions.html Application of genetic material (usually DNA) into cells in order to permanently correct an inherited disease or acquired disease. C15238 Therapeutic or Preventive Procedure Gene Therapy Gene Therapy C0017296 CDISC CTRP Application of genetic material into cells in order to correct an inherited or acquired disease. Treatment of human disease by gene transfer. Treatment that alters a gene. In studies of gene therapy for cancer, researchers are trying to improve the body's natural ability to fight the disease or to make the cancer cells more sensitive to other kinds of therapy. Gene_Therapy Gene therapy techniques attempt to replace a faulty or missing gene associated with a particular disease, mediate localized delivery of a protein producing specified therapeutic effects, or introduce new cellular functions. DNA Therapy GENETIC Gene Therapy Gene Transfer Procedure Gene transfer Genetic Intervention, Genetic Molecular Biology, Gene Therapy gene therapy Gene Therapy Genetic https://prsinfo.clinicaltrials.gov/definitions.html A multidisciplinary field of inquiry that examines the costs, quality, accessibility, delivery, organization, financing, and outcomes of health care services. One or more interventions for evaluating the delivery, processes, management, organization, or financing of healthcare. C15245 Research Activity Health Services Research C0018757 CDISC A type of study designed to evaluate the delivery, processes, management, organization or financing of health care. (ClinicalTrials.gov) Health_Services_Research HEALTH SERVICES RESEARCH Health Services Research Health Services Research One or more interventions for evaluating the delivery, processes, management, organization, or financing of healthcare. https://prsinfo.clinicaltrials.gov/definitions.html A diagnostic or treatment procedure performed by manual and/or instrumental means, often involving an incision and the removal or replacement of a diseased organ or tissue; of or relating to or involving or used in surgery or requiring or amenable to treatment by surgery. C15329 Health Care Activity Surgical Procedure Surgical Procedure C0543467 CPTAC CTRP NICHD A procedure to remove or repair a part of the body or to find out whether disease is present. An operation. Surgical_Procedure Surgical Procedure Surgery Surgically Treated Operation Surgery Surgical Surgical Interventions Surgical Procedure Surgical Procedures Surgically Type of Surgery surgery Surgical Procedure https://prsinfo.clinicaltrials.gov/definitions.html A clinical research protocol designed to test a new biomedical intervention in a small group of people for the first time. A Phase I trial can be to establish the toxicity of a new treatment with escalating intensity of the treatment administered and/or to determine the side effects of a new treatment for a particular indication in subjects. Includes initial studies to determine the metabolism and pharmacologic actions of drugs in humans, the side effects associated with increasing doses, and to gain early evidence of effectiveness; may include healthy participants and/or patients. C15600 Research Activity Phase I Trial C0920321 CDISC CDISC-GLOSS The first step in testing a new treatment in humans. These studies test the best way to give a new treatment (for example, by mouth, intravenous infusion, or injection) and the best dose. The dose is usually increased a little at a time in order to find the highest dose that does not cause harmful side effects. Because little is known about the possible risks and benefits of the treatments being tested, phase I trials usually include only a small number of patients who have not been helped by other treatments. The initial introduction of an investigational new drug into humans. Phase 1 studies are typically closely monitored and may be conducted in patients or normal volunteer subjects. NOTE: These studies are designed to determine the metabolism and pharmacologic actions of the drug in humans, the side effects associated with increasing doses, and, if possible, to gain early evidence on effectiveness. During Phase 1, sufficient information about the drug's pharmacokinetics and pharmacological effects should be obtained to permit the design of well-controlled, scientifically valid Phase 2 studies. The total number of subjects and patients included in Phase 1 studies varies with the drug, but is generally in the range of 20 to 80. Phase 1 studies also include studies of drug metabolism, structure-activity relationships, and mechanism of action in humans, as well as studies in which investigational drugs are used as research tools to explore biological phenomena or disease processes. [after FDA CDER handbook, ICH E8] The initial introduction of an investigational new drug into humans. Phase 1 studies are typically closely monitored and may be conducted in patients or normal volunteer subjects. NOTE: These studies are designed to determine the metabolism and pharmacologic actions of the drug in humans, the side effects associated with increasing doses, and, if possible, to gain early evidence on effectiveness. During Phase 1, sufficient information about the drug's pharmacokinetics and pharmacological effects should be obtained to permit the design of well-controlled, scientifically valid, Phase 2 studies. The total number of subjects and patients included in Phase I studies varies with the drug, but is generally in the range of 20 to 80. Phase 1 studies also include studies of drug metabolism, structure-activity relationships, and mechanism of action in humans, as well as studies in which investigational drugs are used as research tools to explore biological phenomena or disease processes. [After FDA CDER Handbook, ICH E8] (CDISC glossary) Phase_I_Trial 1 Clinical Trials, Phase I Early-Stage Clinical Trials PHASE I TRIAL Phase 1 Study Phase I Clinical Trials Phase I Protocol Phase I Study Phase I Trial Trial Phase 1 phase 1 phase I trial Phase I Trial Includes initial studies to determine the metabolism and pharmacologic actions of drugs in humans, the side effects associated with increasing doses, and to gain early evidence of effectiveness; may include healthy participants and/or patients. https://prsinfo.clinicaltrials.gov/definitions.html A clinical research protocol designed to study a biomedical or behavioral intervention in a larger group of people (several hundred), to evaluate the drug's effectiveness for a particular indication in patients with the disease or condition under study, and to determine the common short-term side effects and risks associated with the intervention. Includes controlled clinical studies conducted to evaluate the effectiveness of the drug for a particular indication or indications in participants with the disease or condition under study and to determine the common short-term side effects and risks. C15601 Research Activity Phase II Trial C0282460 CDISC CDISC-GLOSS A study to test whether a new treatment has an anticancer effect (for example, whether it shrinks a tumor or improves blood test results) and whether it works against a certain type of cancer. Controlled clinical studies conducted to evaluate the effectiveness of the drug for a particular indication or indications in patients with the disease or condition under study and to determine the common short-term side effects and risks associated with the drug. NOTE: Phase 2 studies are typically well controlled, closely monitored, and conducted in a relatively small number of patients, usually involving no more than several hundred subjects. [after FDA CDER handbook, ICH E8] Phase 2. Controlled clinical studies conducted to evaluate the effectiveness of the drug for a particular indication or indications in patients with the disease or condition under study and to determine the common short-term side effects and risks associated with the drug. NOTE: Phase 2 studies are typically well controlled, closely monitored, and conducted in a relatively small number of patients, usually involving no more than several hundred subjects. [After FDA CDER Handbook, ICH E8] (CDISC glossary) Phase_II_Trial 2 Clinical Trials, Phase II PHASE II TRIAL Phase 2 Study Phase II Clinical Trial Phase II Protocol Phase II Study Phase II Trial Trial Phase 2 phase 2 phase II trial Phase II Trial Includes controlled clinical studies conducted to evaluate the effectiveness of the drug for a particular indication or indications in participants with the disease or condition under study and to determine the common short-term side effects and risks. https://prsinfo.clinicaltrials.gov/definitions.html A clinical research protocol designed to investigate the efficacy of the biomedical or behavioral intervention in large groups of human subjects (from several hundred to several thousand), to confirm efficacy, to monitor adverse reactions to the new medication or treatment regimen with respect to long-term use and by comparing the intervention to other standard or experimental interventions as well as to a placebo. Includes trials conducted after preliminary evidence suggesting effectiveness of the drug has been obtained, and are intended to gather additional information to evaluate the overall benefit-risk relationship of the drug. C15602 Research Activity Phase III Trial C0282461 CDISC CDISC-GLOSS A study to compare the results of people taking a new treatment with the results of people taking the standard treatment (for example, which group has better survival rates or fewer side effects). In most cases, studies move into phase III only after a treatment seems to work in phases I and II. Phase III trials may include hundreds of people. Phase 3. Studies are expanded controlled and uncontrolled trials. They are performed after preliminary evidence suggesting effectiveness of the drug has been obtained, and are intended to gather the additional information about effectiveness and safety that is needed to confirm efficacy and evaluate the overall benefit-risk relationship of the drug and to provide an adequate basis for physician labeling. NOTE: Phase 3 studies usually include from several hundred to several thousand subjects. [After FDA CDER Handbook, ICH E8] (CDISC glossary) Studies are expanded controlled and uncontrolled trials. They are performed after preliminary evidence suggesting effectiveness of the drug has been obtained and are intended to gather the additional information about effectiveness and safety that is needed to confirm efficacy and evaluate the overall benefit-risk relationship of the drug and to provide an adequate basis for physician labeling. NOTE: Phase 3 studies usually include from several hundred to several thousand subjects. [after FDA CDER handbook, ICH E8] Phase_III_Trial 3 Clinical Trials, Phase III PHASE III TRIAL Phase 3 Study Phase III Clinical Trial Phase III Protocol Phase III Study Phase III Trial Phase III Trials Trial Phase 3 phase 3 phase III trial Phase III Trial Includes trials conducted after preliminary evidence suggesting effectiveness of the drug has been obtained, and are intended to gather additional information to evaluate the overall benefit-risk relationship of the drug. https://prsinfo.clinicaltrials.gov/definitions.html A randomized, controlled trial that is designed to evaluate the long-term safety and efficacy of a drug for a given indication. Often they are designed to study side effects that may have become apparent after the phase III study was completed. Studies of FDA-approved drugs to delineate additional information including the drug's risks, benefits, and optimal use. C15603 Research Activity Phase IV Trial C0282462 CDISC CDISC-GLOSS After a treatment has been approved and is being marketed, it is studied in a phase IV trial to evaluate side effects that were not apparent in the phase III trial. Thousands of people are involved in a phase IV trial. Phase 4. Postmarketing (Phase 4) studies to delineate additional information about the drug's risks, benefits, and optimal use that may be requested by regulatory authorities in conjunction with marketing approval. NOTE: These studies could include, but would not be limited to, studying different doses or schedules of administration than were used in Phase 2 studies, use of the drug in other patient populations or other stages of the disease, or use of the drug over a longer period of time. [After FDA CDER Handbook, ICH E8] (CDISC glossary) Post approval studies to delineate additional information about the drug's risks, benefits, and optimal use that may be requested by regulatory authorities in conjunction with marketing approval. NOTE: These studies could include, but would not be limited to, studying different doses or schedules of administration than were used in Phase 2 studies, use of the drug in other patient populations or other stages of the disease, or use of the drug over a longer period of time. [after FDA CDER handbook, ICH E8] Phase_IV_Trial 4 Clinical Trials, Phase IV PHASE IV TRIAL Phase 4 Study Phase IV Clinical Trials Phase IV Study Phase IV Trial Trial Phase 4 phase 4 phase IV trial Phase IV Trial Studies of FDA-approved drugs to delineate additional information including the drug's risks, benefits, and optimal use. https://prsinfo.clinicaltrials.gov/definitions.html A clinical research protocol designed to study the safety, dosage levels and response to new treatment. Phase I/II trials combine a Phase I and a Phase II trial of the same treatment into a single protocol. Trials that are a combination of phases 1 and 2. C15693 Research Activity Phase I/II Trial C1519043 CDISC A class of clinical study that combines elements characteristic of traditional Phase I and Phase II trials. See also Phase I, Phase II. A trial to study the safety, dosage levels, and response to a new treatment. Phase_I_II_Trial 1-2 PHASE I/II TRIAL Phase I/II Trial Phase I/II trial Trial Phase 1-2 Trial Phase 1/2 Phase I/II Trial Trials that are a combination of phases 1 and 2. https://prsinfo.clinicaltrials.gov/definitions.html A type of clinical study that combines elements characteristic of traditional Phase II and Phase III trials. Trials that are a combination of phases 2 and 3. C15694 Research Activity Phase II/III Trial C1519042 CDISC A class of clinical study that combines elements characteristic of traditional Phase II and Phase III trials. A trial to study response to a new treatment and the effectiveness of the treatment compared with the standard treatment regimen. Phase_II_III_Trial 2-3 PHASE II/III TRIAL Phase II/III Trial Trial Phase 2-3 Trial Phase 2/3 phase II/III trial Phase II/III Trial Trials that are a combination of phases 2 and 3. https://prsinfo.clinicaltrials.gov/definitions.html Fundamental research designed to obtain or increase general scientific knowledge. One or more interventions for examining the basic mechanism of action (for example, physiology or biomechanics of an intervention). C15714 Research Activity Basic Research C0681833 CDISC A type of study designed to examine the basic mechanism of action (e.g., physiology, biomechanics) of an intervention. (ClinicalTrials.gov) Basic_Science BASIC SCIENCE Basic Research Basic Science Basic Science Research Basic Research One or more interventions for examining the basic mechanism of action (for example, physiology or biomechanics of an intervention). https://prsinfo.clinicaltrials.gov/definitions.html Studies among cancer patients and healthy populations that involve no intervention or alteration in the status of the participants. C16084 Research Activity Observational Study C1518527 CDISC A type of study in which individuals are observed or certain outcomes are measured. No attempt is made to affect the outcome (for example, no treatment is given). Studies in which biomedical and/or health outcomes are assessed in pre-defined groups of individuals. Subjects in the study may receive diagnostic, therapeutic, or other interventions, but the investigator does not assign specific interventions to the subjects of the study. Observational_Study OBSERVATIONAL Observational Study Observational Trial observational study Observational Study Primary disease(s) or condition(s) being studied in the trial, or the focus of the study. (clinicaltrials.gov) The disease, disorder, syndrome, illness, or injury that is being studied. On ClinicalTrials.gov, conditions may also include other health-related issues, such as lifespan, quality of life, and health risks. The name(s) of the disease(s) or condition(s) studied in the clinical study, or the focus of the clinical study. Use, if available, appropriate descriptors from NLM's Medical Subject Headings (MeSH)-controlled vocabulary thesaurus or terms from another vocabulary, such as the Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT), that has been mapped to MeSH within the Unified Medical Language System (UMLS) Metathesaurus. C161319 Qualitative Concept Condition or Disease under Study CDISC Primary disease(s) or condition(s) being studied in the trial, or the focus of the study. (clinicaltrials.gov) Condition or Disease under Study Primary Disease or Condition Being Studied in the Trial, or the Focus of the Study health condition(s) or problem(s) studied target disease condition Condition or Disease under Study The disease, disorder, syndrome, illness, or injury that is being studied. On ClinicalTrials.gov, conditions may also include other health-related issues, such as lifespan, quality of life, and health risks. https://clinicaltrials.gov/ct2/about-studies/glossary The name(s) of the disease(s) or condition(s) studied in the clinical study, or the focus of the clinical study. Use, if available, appropriate descriptors from NLM's Medical Subject Headings (MeSH)-controlled vocabulary thesaurus or terms from another vocabulary, such as the Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT), that has been mapped to MeSH within the Unified Medical Language System (UMLS) Metathesaurus. https://prsinfo.clinicaltrials.gov/definitions.html health condition(s) or problem(s) studied https://www.who.int/ictrp/network/trds/en/ 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 A type of eligibility criteria that indicates the age a person must be to participate in a clinical study. How long something has existed; elapsed time since birth. C25150 Organism Attribute Age C0001779 CDISC FDA NICHD How long something has existed; elapsed time since birth. (NCI) The time elapsed since birth. Age Chronological Age AGE Age Aged Chronological Age Postnatal Age age Age A type of eligibility criteria that indicates the age a person must be to participate in a clinical study. https://clinicaltrials.gov/ct2/about-studies/glossary A formal document that describes a complete plan of research activity in the framework of a clinical study; specifically, the study objective(s), design, methodology, eligibility requests for prospective subjects and controls; intervention regimen(s), proposed methods of analysis of data; statistical considerations, and organization of the study. The protocol usually also provides the background and rationale for the trial, but these could be represented in other protocol referenced documents. C25320 Intellectual Product Clinical Study Protocol C1507394 BRIDG CDISC-GLOSS CareLex A detailed plan of a scientific or medical experiment, treatment, or procedure. In clinical trials, it states what the study will do, how it will be done, and why it is being done. It explains how many people will be in the study, who is eligible to take part in it, what study drugs or other interventions will be given, what tests will be done and how often, and what information will be collected. A discrete, structured plan (that persists over time) of a formal investigation to assess the utility, impact, pharmacological, physiological, and/or psychological effects of a particular treatment, procedure, drug, device, biologic, food product, cosmetic, care plan, or subject characteristic. NOTE(S): The term "protocol" is somewhat overloaded and must be qualified to provide semantic context. Therefore the term "study protocol" was chosen to disambiguate it from other protocols. In previous versions of BRIDG, there was one class for StudyProtocol. However this too represented multiple distinct aspects of the semantics of study protocol, each of which have now been split into separate classes:- The StudyProtocol class represents the content of the study protocol and can exist even before the information is put into document form. - The details of the structured plan for the study protocol are represented by the StudyProtocolVersion, so named because any aspect of the definition can change from version to version. These details include, but are not limited to, the characteristics, specifications, objective(s), background, the pre-study/study/post-study portions of the plan (including the design, methodology, statistical considerations, organization).- The protocol and its versions can each be represented in document form, respectively StudyProtocolDocument and StudyProtocolDocumentVersion. A StudyProtocolDocument groups the various document versions (StudyProtocolDocumentVersions).- The conduct of a study based on a study protocol definition is represented by the StudyExecution class. A formal document that describes a complete plan of research activity in the framework of a clinical study; specifically, the study objective(s), design, methodology, eligibility requests for prospective subjects and controls; intervention regimen(s), proposed methods of analysis of data; statistical considerations, and organization of the study. The protocol usually also provides the background and rationale for the trial, but these could be represented in other protocol referenced documents. [NCI] See protocol. Protocol Clinical Study Protocol Clinical Trial Protocol Full Protocol Prot Protocol Protocol Amendment Study Protocol StudyProtocol Trial Protocol clinical protocol protocol Clinical Study Protocol A person or organization that supports or champions something. C48355 Human Sponsor C1711305 Sponsor Applicant Sponsor Sponsor A type of study designed to evaluate method(s) aimed at identifying a disease or condition. One or more interventions are being evaluated for identifying a disease or health condition. C49653 Research Activity Diagnosis Study C1704656 CDISC A type of study designed to evaluate intervention(s) aimed at identifying a disease or condition. Diagnosis_Study DIAGNOSIS Diagnosis Study Diagnostic Study Diagnosis Study One or more interventions are being evaluated for identifying a disease or health condition. https://prsinfo.clinicaltrials.gov/definitions.html A type of study protocol designed to evaluate intervention(s) for disease treatment. One or more interventions are being evaluated for treating a disease, syndrome, or condition. C49656 Research Activity Treatment Study C3161471 CDISC A type of study designed to evaluate intervention(s) for treatment of disease, syndrome or condition. Treatment_Study TREATMENT Therapy Trial Treatment Study Treatment Study One or more interventions are being evaluated for treating a disease, syndrome, or condition. https://prsinfo.clinicaltrials.gov/definitions.html A type of study protocol designed to evaluate intervention(s) for disease prevention. One or more interventions are being assessed for preventing the development of a specific disease or health condition. C49657 Research Activity Prevention Study C1706420 CDISC A type of study designed to identify actions necessary to permanently eliminate or reduce the long-term risk to human life as a result of a particular medication or treatment regimen. Prevention_Study PREVENTION Prevention Study Preventive Clinical Trial Prophylaxis Study Prevention Study One or more interventions are being assessed for preventing the development of a specific disease or health condition. https://prsinfo.clinicaltrials.gov/definitions.html The number of subjects entered in a clinical trial. C49692 Group Attribute Planned Subject Number C1709561 CDISC CDISC-GLOSS The number of subjects in a class or group (including the total for the entire trial) intended to be enrolled in a trial to reach the planned sample size. Target enrollments are set so that statistical and scientific objectives of a trial will have a likelihood of being met as determined by agreement, algorithm, or other specified process. The planned number of subjects to be entered in a clinical trial. (NCI) Planned_Subject_Number Anticipated Enrollment PLANSUB Planned Enrollment Planned Number of Subjects Planned Subject Number Target Enrollment target enrollment target number target size Planned Subject Number https://prsinfo.clinicaltrials.gov/definitions.html https://www.who.int/ictrp/network/trds/en/ The distribution of resources over various time periods, products, operations, or investments. The method by which participants are assigned to arms in a clinical trial. C52580 Activity Allocation C1706778 CDISC The process of assigning subjects to particular treatment groups or cohorts in a clinical study. Allocation Allocation Subject Allocation Allocation https://www.clinicaltrials.gov/ct2/about-studies/glossary The method by which participants are assigned to arms in a clinical trial. https://prsinfo.clinicaltrials.gov/definitions.html Information regarding the means of contacting a person or group. C60776 Conceptual Entity Contact Information C1880174 Contact_Information Contact Info Contact Information Contact Information An entity such as an individual, company, institution, group, or organization which takes responsibility for the initiation, management, and/or financing of a clinical study. The sponsor does not actually conduct the investigation unless the sponsor is a sponsor-investigator. A person other than an individual (e.g., corporation or agency) that uses one or more of its own employees to conduct research it has initiated is considered to be a sponsor, and the employees are considered to be investigators. [21 CFR P.50.3(k)] [21 CFR P.50.102(j)] [21 CFR P.312.3] C70793 Health Care Related Organization Clinical Study Sponsor C2347796 CDISC CDISC-GLOSS CareLex An entity that is responsible for the initiation, management, and/or financing of a clinical study. An entity that is responsible for the initiation, management, and/or financing of a clinical study.[NCI] An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. NOTE: If there is also a secondary sponsor, the responsible entity would be considered the primary sponsor. A corporation or agency whose employees conduct the investigation is considered a sponsor and the employees are considered investigators. [After ICH E6, WHO, 21 CFR 50.3 (e), and after IDMP] See also secondary sponsor. Clinical_Study_Sponsor CLINICAL STUDY SPONSOR Clinical Study Sponsor SPONSOR Sponsor Study Sponsor sponsor Clinical Study Sponsor The formal plan of an experiment or research activity, including the objective, rationale, design, materials and methods for the conduct of the study; intervention description, and method of data analysis. The written description of the clinical study, including objective(s), design, and methods. It may also include relevant scientific background and statistical considerations (if the protocol document includes the statistical analysis plan, use "Study Protocol with SAP and/or ICF" option). Note: All amendments approved by a human subjects protection review board (if applicable), before the time of submission and that apply to all clinical trial Facility Locations must be included. C70817 Intellectual Product Study Protocol C2348563 CDISC The formal plan of an experiment or research activity, including the objective, rationale, design, materials and methods for the conduct of the study, intervention description, and method of data analysis. Study_Protocol Protocol Study Protocol Study Protocol https://prsinfo.clinicaltrials.gov/definitions.html The written description of the clinical study, including objective(s), design, and methods. It may also include relevant scientific background and statistical considerations (if the protocol document includes the statistical analysis plan, use "Study Protocol with SAP and/or ICF" option). Note: All amendments approved by a human subjects protection review board (if applicable), before the time of submission and that apply to all clinical trial Facility Locations must be included. https://prsinfo.clinicaltrials.gov/results_definitions.html A clinical study that is designed using a procedure in which one or more parties to the study [subject(s), investigator(s), monitor, or/and data analyst(s)] are kept unaware of the treatment assignment(s). C70840 Research Activity Blinded Clinical Study C2347038 CDISC-GLOSS A study in which the subject, the investigator, or anyone assessing the outcome is unaware of the treatment assignment(s). NOTE: Blinding is used to reduce the potential for bias. [Modified ICH E6 Glossary] See also blinding/masking, double-blind study, single-blind study, triple-blind study; contrast with open-label or unblinded study. A type of study in which the patients (single-blinded) or the patients and their doctors (double-blinded) do not know which drug or treatment is being given. The opposite of a blinded study is an open label study. Blinded_Clinical_Study Blind Clinical Study Blinded Clinical Study Blinded Clinical Trial Masked Clinical Study blinded study Blinded Clinical Study Clinical studies testing the efficacy of devices, techniques, procedures, or tests for the purpose of detecting the presence of disease, usually before there are any symptoms. One or more interventions are assessed or examined for identifying a condition, or risk factors for a condition, in people who are not yet known to have the condition or risk factor. C71485 Research Activity Screening Study C2348164 CDISC CDISC-GLOSS A type of study designed to assess or examine methods of identifying a condition (or risk factors for a condition) in people who are not yet known to have the condition (or risk factor). (Clinicaltrials.gov) Trials conducted to detect persons with early, mild, and asymptomatic disease. Screening_Study SCREENING Screening Study Screening Trial screening trials Screening Study One or more interventions are assessed or examined for identifying a condition, or risk factors for a condition, in people who are not yet known to have the condition or risk factor. https://prsinfo.clinicaltrials.gov/definitions.html Clinical studies intended to improve the comfort and quality of life for the patient using drugs, nutritional, dietary, behavioral or other interventions. One or more interventions are evaluated for maximizing comfort, minimizing side effects, or mitigating against a decline in the participant's health or function. C71486 Research Activity Supportive Care Study C2348611 CDISC A type of study designed to evaluate one or more interventions where the primary intent is to maximize comfort, minimize side effects or mitigate against a decline in the subject's health or function. In general, supportive care interventions are not intended to cure a disease. (ClinicalTrials.gov) Supportive_Care_Study SUPPORTIVE CARE Supportive Care Study Supportive Care Trial Supportive Care Study One or more interventions are evaluated for maximizing comfort, minimizing side effects, or mitigating against a decline in the participant's health or function. https://prsinfo.clinicaltrials.gov/definitions.html A type of clinical study in which two or more treatments are given alone and in combination, such that all possible combinations are represented across the treatment arms, and are compared in parallel against the study control group. Two or more interventions, each alone and in combination, are evaluated in parallel against a control group C82638 Research Activity Factorial Study C2826344 CDISC Two or more interventions, each alone or in combination, are evaluated in parallel against a control group. This study design allows for the comparison of active drug to placebo, presence of drug-drug interactions, and comparison of active drugs against each other. Factorial_Study FACTORIAL Factorial Study Factorial Study Two or more interventions, each alone and in combination, are evaluated in parallel against a control group https://prsinfo.clinicaltrials.gov/definitions.html Any of two or more parties working jointly towards a common goal. C84336 Conceptual Entity Collaborator C2827395 Collaborator Collaborator The country in which the test is conducted. C90467 Geographic Area Test Facility Country C2983675 CDISC The country of the place in which a nonclinical laboratory study takes place, i.e., actually uses the test article in a test system. Testing facility includes any establishment required to register under section 510 of the act that conducts nonclinical laboratory studies and any consulting laboratory described in section 704 of the act that conducts such studies. Testing facility encompasses only those operational units that are being or have been used to conduct nonclinical laboratory studies. (FDA) TFCNTRY Test Facility Country Test Facility Country The geographic area in which a test is conducted. C90468 Geographic Area Test Facility Location C2983676 CDISC The geographic area of the place in which a nonclinical laboratory study takes place, i.e., actually uses the test article in a test system. Testing facility includes any establishment required to register under section 510 of the act that conducts nonclinical laboratory studies and any consulting laboratory described in section 704 of the act that conducts such studies. Testing facility encompasses only those operational units that are being or have been used to conduct nonclinical laboratory studies. (FDA) TSTFLOC Test Facility Location Test Facility Location The name of the place in which a test is conducted. C90469 Intellectual Product Test Facility Name C2983677 CDISC The name of the place in which a nonclinical laboratory study takes place, i.e., actually uses the test article in a test system. Testing facility includes any establishment required to register under section 510 of the act that conducts nonclinical laboratory studies and any consulting laboratory described in section 704 of the act that conducts such studies. Testing facility encompasses only those operational units that are being or have been used to conduct nonclinical laboratory studies. (FDA) TSTFNAM Test Facility Name Test Facility Name A condition that is a focus of the study. C93360 Qualitative Concept Study Condition C2985574 BRIDG A condition that is a focus of the study. Study Condition StudyCondition Study Condition Studies in which individuals are assigned by an investigator based on a protocol to receive specific interventions. Subjects may receive diagnostic, therapeutic or other types of interventions. The assignment of the intervention may or may not be random. The individuals are then followed and biomedical and/or health outcomes are assessed. C98388 Research Activity Interventional Study C3274035 CDISC CDISC-GLOSS A trial which intervenes with the inviolability of the trial subject for the purpose of the investigation. For example, the administration of an investigational medical product to the trial subject or use of some extra means of intervention (i.e., samples, tests, or questionnaires) that would not otherwise be used. [Clinical Trial Directive EC/20/2001 definitions] Studies in which individuals are assigned by an investigator based on a protocol to receive specific interventions. Subjects may receive diagnostic, therapeutic or other types of interventions. The assignment of the intervention may or may not be random. The individuals are then followed and biomedical and/or health outcomes are assessed. INTERVENTIONAL Interventional Study interventional clinical trial Interventional Study A sequence of letters, numbers, or other characters that uniquely identifies a clinical trial within a clinical trial registry. C98714 Intellectual Product Clinical Trial Registry Identifier C3274381 CDISC Identification numbers assigned to the protocol by clinicaltrials.gov, EudraCT, or other registries. Clinical Trial Registry Identifier REGID Registry Identifier Trial Identifying Number Clinical Trial Registry Identifier https://www.who.int/ictrp/network/trds/en/ An investigational drug product (including biological product) available through expanded access for patients who do not qualify for enrollment in a clinical trial. Expanded Access includes all expanded access types under section 561 of the Federal Food, Drug, and Cosmetic Act: (1) for individual patients, including emergency use; (2) for intermediate-size patient populations; and (3) under a treatment IND or treatment protocol. Studies that provide a means for obtaining an experimental drug or device for patients who are not adequately treated by existing therapy, who do not meet the eligibility criteria for enrollment, or who are otherwise unable to participate in another clinical study. Expanded Access studies include individual-patient IND, treatment IND, compassionate use, emergency use or continued access. C98722 Research Activity Expanded Access Study C3274389 CDISC Studies that provide a means for obtaining an experimental drug or device for patients who are not adequately treated by existing therapy, who do not meet the eligibility criteria for enrollment, or who are otherwise unable to participate in another clinical study. Expanded Access studies include individual-patient IND, treatment IND, compassionate use, emergency use or continued access. EXPANDED ACCESS Expanded Access Study Expanded Access Study https://prsinfo.clinicaltrials.gov/expanded_access_definitions.html An investigational drug product (including biological product) available through expanded access for patients who do not qualify for enrollment in a clinical trial. Expanded Access includes all expanded access types under section 561 of the Federal Food, Drug, and Cosmetic Act: (1) for individual patients, including emergency use; (2) for intermediate-size patient populations; and (3) under a treatment IND or treatment protocol. https://prsinfo.clinicaltrials.gov/definitions.html For each intervention studied in the clinical study, the general type of intervention. The kind of product or procedure studied in a trial. C98747 Functional Concept Intervention Type C3274412 CDISC The kind of product or procedure studied in a trial. INTTYPE Intervention Type intervention Intervention Type For each intervention studied in the clinical study, the general type of intervention. https://prsinfo.clinicaltrials.gov/definitions.html intervention http://www.icmje.org/recommendations/ http://www.who.int/ictrp/network/trds/en/index.html The primary measurement(s) or observation(s) used to measure the effect of experimental variables in a study, or for observational studies, to describe patterns of diseases or traits or associations with exposures, risk factors or treatment. These are the outcome measures used to assess the primary objective(s). C98772 Intellectual Product Primary Outcome Measure C3274433 CDISC The primary measurement(s) or observation(s) used to measure the effect of experimental variables in a study, or for observational studies, to describe patterns of diseases or traits or associations with exposures, risk factors or treatment. These are the outcome measures used to assess the primary objective(s). OUTMSPRI PRIMARY OUTCOME MEASURE Primary Outcome Measure Primary Outcome Measure Other key measures that will be used to evaluate the intervention(s) or, for observational studies, that are a focus of the study. These are the outcome measures used to assess the secondary objective(s). C98781 Intellectual Product Secondary Outcome Measure C3274440 CDISC Secondary measures that will be used to evaluate the intervention(s) or, for observational studies, that are a focus of the study. These are the outcome measures used to assess the secondary objective(s). OUTMSSEC SECONDARY OUTCOME MEASURE Secondary Outcome Measure Secondary Outcome Measure Any untoward or unfavorable medical occurrence in a participant, including any abnormal sign (for example, abnormal physical exam or laboratory finding), symptom, or disease, temporally associated with the participant’s participation in the research, whether or not considered related to the participant’s participation in the research a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event. Melanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'. YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device. YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention. YH: In development of OAE, we initially use vaccine adverse event as our use case. A vaccine adverse event is associated with a vaccination (i.e. a medical intervention), regardless of whether it is considered vaccine-related, and includes any side effect, injury, toxicity, or sensitivity reaction or significant failure of immunization (i.e., a pharmacologic action). Ref: Baylor NW and Midthum K. Regulation and testing of vaccines. In: Vaccines (Editors: Plotkin S, Orenstein W, and Offit P). 2008. p1623. YH: The current term 'adverse event' is different from the term definition shown in our paper: He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. OAE: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full lenghth conference proceeding paper. We made the name changing in order to make OAE cover the broader sense of the 'adverse event' which does not assume definite causal effect between an adverse event and a medical intervention. In current definition, the adverse event emphasizes the time association and assumes a likelihood of such a causal association. This term 'adverse event' is stil under the OGMS:pathological bodily process. The 'adverse event' defined in the above paper has now been changed to a new term: 'causal adverse event'. See more information in the new publication: Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29 doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740. YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events. YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'. Yongqun He AE adverse reaction WEB: http://en.wikipedia.org/wiki/Adverse_event WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068 The OAE official website is: http://www.oae-ontology.org/. adverse event Any untoward or unfavorable medical occurrence in a participant, including any abnormal sign (for example, abnormal physical exam or laboratory finding), symptom, or disease, temporally associated with the participant’s participation in the research, whether or not considered related to the participant’s participation in the research https://prsinfo.clinicaltrials.gov/results_definitions.html A process or action that is the focus of a clinical study. Interventions include drugs, medical devices, procedures, vaccines, and other products that are either investigational or already available. Interventions can also include noninvasive approaches, such as education or modifying diet and exercise. medical intervention is a planned process that has the goal of diagnosing, preventing or relieving illness or injury. The act of intervening, interfering or interceding with the intent of modifying the outcome. In medicine, an intervention is usually undertaken to help treat or cure a condition. For example, "Acupuncture as a therapeutic intervention is widely practiced in the United States," Reference: http://www.medterms.com/script/main/art.asp?articlekey=34214 . Some interventions can be used for diagnosis. The act of intervening, interfering or interceding with the intent of modifying the outcome. In medicine, an intervention is usually undertaken to help treat or cure a condition. For example, "Acupuncture as a therapeutic intervention is widely practiced in the United States," Reference: http://www.medterms.com/script/main/art.asp?articlekey=34214 . Some interventions can be used for diagnosis. YH WEB: http://wiki.answers.com/Q/What_is_medical_intervention Intervention(s) medical intervention https://prsinfo.clinicaltrials.gov/definitions.html A process or action that is the focus of a clinical study. Interventions include drugs, medical devices, procedures, vaccines, and other products that are either investigational or already available. Interventions can also include noninvasive approaches, such as education or modifying diet and exercise. https://www.clinicaltrials.gov/ct2/about-studies/glossary Intervention(s) http://www.icmje.org/recommendations/ http://www.who.int/ictrp/network/trds/en/index.html a medical intervention where a patient is administered with a drug YH drug administration a medical intervention that is used for therapeutic purpose YH therapeutic intervention a medical intervention that refers to any series of pre-defined steps that should be followed to achieve a desired result. YH, SS WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm medical procedure planned process planned process Injecting mice with a vaccine in order to test its efficacy A processual entity that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) http://purl.obolibrary.org/obo/obi.owl planned process planned process 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 assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method assay responsible party role he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study Person: Jennifer Fostel responsible party OBI responsible party role intervention design PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study. A description of the manner in which the clinical trial will be conducted. An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. Philppe Rocca-Serra OBI branch derived Interventional Study Design intervention model intervention design A description of the manner in which the clinical trial will be conducted. https://prsinfo.clinicaltrials.gov/definitions.html investigation agent role The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009) GROUP: Role Branch investigator OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. study person role Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) investigation agent role sponsor role a responsible party role involved with any of the following activities: initiating, managing and funding a study Person: Jennifer Fostel sponsor CDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigators sponsor role organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization protocol PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol protocol informed consent process A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#informed 2009/09/28 Alan Ruttenberg. Fucoidan-use-case informed consent process device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. device country name A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Website: http://en.wikipedia.org/wiki/Country Specimen Collection Location - Country NIAID GSCID-BRC country name selection criterion rats should be aged between 6 and 8 weeks and weight between 180-250grams A directive information entity which defines and states a principle of standard by which selection process may take place. Person: Philippe Rocca-Serra selection rule OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/ selection criterion selection PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria. this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary) Person: Philippe Rocca-Serra selection process OBI selection value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification age group inclusion criterion "18-33 years old" A type of eligibility criteria that indicates the age a person must be to participate in a clinical study. This may be indicated by a specific age or the following age groups. The age groups are: Child (birth-17), Adult (18-64), Older Adult (65+). An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process. Mathias Brochhausen #839 ages eligible for study age group inclusion criterion https://www.who.int/ictrp/network/trds/en/ A type of eligibility criteria that indicates the age a person must be to participate in a clinical study. This may be indicated by a specific age or the following age groups. The age groups are: Child (birth-17), Adult (18-64), Older Adult (65+). https://clinicaltrials.gov/ct2/about-studies/glossary minimum age value specification A value specifcation that specifies the youngest age when specifying an age range. The numerical value, if any, for the minimum age a potential participant must meet to be eligible for the clinical study. Mathias Brochhausen minimum age minimum age value specification The numerical value, if any, for the minimum age a potential participant must meet to be eligible for the clinical study. https://prsinfo.clinicaltrials.gov/definitions.html maximum age value specification A value specifcation that specifies the oldest age when specifying an age range. The numerical value, if any, for the maximum age a potential participant can be to be eligible for the clinical study. Mathias Brochhausen maximum age maximum age value specification The numerical value, if any, for the maximum age a potential participant can be to be eligible for the clinical study. https://prsinfo.clinicaltrials.gov/definitions.html sex inclusion criterion "included males and females", "included male patients" A type of eligibility criteria that indicates the sex of people who may participate in a clinical study (all, female, male). Sex is a person's classification as female or male based on biological distinctions. Sex is distinct from gender-based eligibility. An inclusion criterion that defines and states one or more sexes which, if met, makes an entity suitable for a given task or participation in a given process. Mathias Brochhausen sexes eligible for study sex inclusion criterion https://www.who.int/ictrp/network/trds/en/ A type of eligibility criteria that indicates the sex of people who may participate in a clinical study (all, female, male). Sex is a person's classification as female or male based on biological distinctions. Sex is distinct from gender-based eligibility. https://clinicaltrials.gov/ct2/about-studies/glossary case-control study design A study design that entails the creation of two types of roles, such that each participant under investigation bears one or the other. What distinguishes the two types of roles is an 'outcome', which is associated with participants that have the case role but not associated with participants that have the control role. A case-control study examines the hypothesis that the presence of the outcome in case participants is associated with an 'exposure' that is not associated with control participants. John Judkins, Bjoern Peters Wikipedia, OBI case-control study design observation design PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. Philippe Rocca-Serra OBI branch derived observation design https://prsinfo.clinicaltrials.gov/definitions.html study design a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design https://prsinfo.clinicaltrials.gov/definitions.html https://www.who.int/ictrp/network/trds/en/ repeated measure design PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations. a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs PlanAndPlannedProcess Branch http://www.holah.karoo.net/experimentaldesigns.htm repeated measure design cross over design PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity. Participants receive one of two (or more) alternative interventions during the initial phase of the study and receive the other intervention during the second phase of the study a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control Philippe Rocca-Serra (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html) cross over design Participants receive one of two (or more) alternative interventions during the initial phase of the study and receive the other intervention during the second phase of the study https://prsinfo.clinicaltrials.gov/definitions.html n-to-1 design N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993). Philippe Rocca-Serra Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm) n-to-1 design parallel group design PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR. A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment Participants are assigned to one of two or more groups in parallel for the duration of the study Philippe Rocca-Serra independent measure design http://www.holah.karoo.net/experimentaldesigns.htm parallel group design Participants are assigned to one of two or more groups in parallel for the duration of the study https://prsinfo.clinicaltrials.gov/definitions.html factorial design PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. Two or more interventions, each alone and in combination, are evaluated in parallel against a control group factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable. Philippe Rocca-Serra http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment) factorial design Two or more interventions, each alone and in combination, are evaluated in parallel against a control group https://prsinfo.clinicaltrials.gov/definitions.html eligibility criterion PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3. A limited list of criteria for selection of participants in the clinical study, provided in terms of inclusion and exclusion criteria and suitable for assisting potential participants in identifying clinical studies of interest. The key requirements that people who want to participate in a clinical study must meet or the characteristics they must have. Eligibility criteria consist of both inclusion criteria (which are required for a person to participate in the study) and exclusion criteria (which prevent a person from participating). Types of eligibility criteria include whether a study accepts healthy volunteers, has age or age group requirements, or is limited by sex an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process. Person: Philippe Rocca-Serra eligibility rule Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group eligibility criterion A limited list of criteria for selection of participants in the clinical study, provided in terms of inclusion and exclusion criteria and suitable for assisting potential participants in identifying clinical studies of interest. https://prsinfo.clinicaltrials.gov/definitions.html The key requirements that people who want to participate in a clinical study must meet or the characteristics they must have. Eligibility criteria consist of both inclusion criteria (which are required for a person to participate in the study) and exclusion criteria (which prevent a person from participating). Types of eligibility criteria include whether a study accepts healthy volunteers, has age or age group requirements, or is limited by sex https://clinicaltrials.gov/ct2/about-studies/glossary inclusion criterion PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) . A type of eligibility criteria. These are the reasons that a person is allowed to participate in a clinical study. an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study. Person: Philippe Rocca-Serra inclusion condition inclusion rule Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group key inclusion criteria inclusion criterion A type of eligibility criteria. These are the reasons that a person is allowed to participate in a clinical study. https://clinicaltrials.gov/ct2/about-studies/glossary key inclusion criteria http://www.icmje.org/recommendations/ https://www.who.int/ictrp/network/trds/en/ exclusion rule PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months. A type of eligibility criteria. These are reasons that a person is not allowed to participate in a clinical study. an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study Person: Philippe Rocca-Serra Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group key exclusion criteria exclusion criterion A type of eligibility criteria. These are reasons that a person is not allowed to participate in a clinical study. https://clinicaltrials.gov/ct2/about-studies/glossary key exclusion criteria http://www.icmje.org/recommendations/ https://www.who.int/ictrp/network/trds/en/ human subject enrollment enlisting familiy members of HIV patients into a study A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent. As with group assignment, should the specified output here be an organism which bears a role Bjoern Peters IEDB criteria come from plan / clinical trial branch human subject enrollment A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T10:18:02Z clinical finding A series of statements representing health-relevant qualities of a patient and of a patient's family. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T10:18:59Z clinical history A representation of a quality of a patient that is (1) recorded by a clinician because the quality is hypothesized to be of clinical significance and (2) refers to qualities obtaining in the patient prior to their becoming detectable in a clinical history taking or physical examination. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:22:44Z preclinical finding A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:21:20Z disease Albert Goldfain creation date: 2009-06-23T11:53:49Z bodily process A bodily process that is clinically abnormal. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:54:29Z pathological bodily process 1. the determination of the nature of a case of disease. 2. the art of distinguishing one disease from another. The representation of a conclusion of a diagnostic process. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T12:42:23Z diagnosis 1. the determination of the nature of a case of disease. 2. the art of distinguishing one disease from another. https://www.clinicaltrialsregister.eu/doc/EU_Clinical_Trials_Register_Glossary.pdf A study design that involves repeated observations of the same entity over time. In the biobank context, longitudinal studies sample a group of people in a given time period, and study them at intervals by the acquisition and analyses of data and/or samples over time. Alice Nzinga longitudinal study design A longitudinal study that aims to study a case-defined population who presently have a certain condition or recepient of a particular treatment that are followed over time and are compared with a similar group who do not have condition. cohort study design A role inhering in an entity realized by social interactions in human society. Mathias Brochhausen Previous definition: A role played by an entity in human social processes. role in human social processes A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law. Mathias Brochhausen Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008. We are aware of the fact that Wikipedia's definition differs from ours by saying that "Legal personality (...) is the characteristic of a non-living entity regarded by law to have the status of personhood" (http://en.wikipedia.org/wiki/Legal_personality) However, Shaw explicates: "In any legal system, certain entities, whether they be individuals or companies, will be regarded as possessing rights and duties enforceable at law. Thus an individual may prosecute or be prosecuted for assault and a company can sue for breach of contract. They are able to do this because the law recognises them as 'legal persons' possessing the capacity to have and to maintain certain rights, and being subject to perform specific duties. (...) In municipal law individuals, limited companies and public corporations are recognized as each possessing a distinct legal personality, the terms of which are circumscribed by the relevant legislation" (Shaw MN: International Law. Sixth Edition. Cambridge University Press, Cambridge, 2008). We hold that Shaw's position is ontological more prolific since it not only allows to explain how groups of individuals become recognized as unities at law, but also how different individuals can hold different legal personality roles (always against the context of one legal system). The latter will proof useful when dealing with the representing comatous patients or minorsat law in ontologies. legal person role A telephone number is a sequence of digits assigned to a fixed-line telephone subscriber station connected to a telephone line or to a wireless electronic telephony device, such as a radio telephone or a mobile telephone, or to other devices for data transmission via the public switched telephone network (PSTN) or other public and private networks. Oliver He phone number https://en.wikipedia.org/wiki/Telephone_number telephone number The textual name of the contact person or organization contact name The medical state or condition of a patient Oliver He, Edison Ong medical state https://en.wikipedia.org/wiki/Medical_state medical condition A centrally registered identifier that is assigned for a specific clinical trial registered in the ClinicalTrials.gov. The format for the ClinicalTrials.gov registry number is “NCT” followed by an 8-digit number, e.g.: NCT00000419. Qingliang Leon Li, Asiyah Yu Lin, Oliver He NCT identifier NCT number National Clinical Trial identifier https://clinicaltrials.gov/ct2/about-site/link-to https://www.nlm.nih.gov/bsd/policy/clin_trials.html USA National Clinical Trial identifier A textual entity that is the title of a clinical trial https://prsinfo.clinicaltrials.gov/definitions.html title of clinical trial A title of clinical trial that is recorded as official https://prsinfo.clinicaltrials.gov/definitions.html full title scientific title official title of clinical trial https://www.who.int/ictrp/network/trds/en/ A title of clinical trial that is meant for lay people understanding https://prsinfo.clinicaltrials.gov/definitions.html brief title lay title public title lay title of clinical trial https://www.who.int/ictrp/network/trds/en/ A person who performs an investigation task and takes the role of an investigator role. investigator An investigator who is involved in a clinical trial and is responsible for ensuring that an investigation is conducted according to the signed investigator statement, the investigational plan, and applicable regulations; for protecting the rights, safety, and welfare of subjects under the investigator's care; and for the control of drugs under investigation. Oliver He https://en.wikipedia.org/wiki/Clinical_investigator clinical investigator The date on which a study starts study start date The (estimated) date on which the clinical study is open for recruitment of participants, or the actual date on which the first participant is enrolled. https://prsinfo.clinicaltrials.gov/definitions.html date of first enrollment study start clinical trial start date date of first enrollment http://www.icmje.org/recommendations/ http://www.who.int/ictrp/network/trds/en/index.html The date on which a study completes The date the final participant was examined or received an intervention for purposes of final collection of data for the primary and secondary outcome measures and adverse events (for example, last participant’s last visit), whether the clinical study concluded according to the pre-specified protocol or was terminated. Oliver He Completion Date study completion study completion date The date the final participant was examined or received an intervention for purposes of final collection of data for the primary and secondary outcome measures and adverse events (for example, last participant’s last visit), whether the clinical study concluded according to the pre-specified protocol or was terminated. https://prsinfo.clinicaltrials.gov/definitions.html Completion Date http://www.icmje.org/recommendations/ http://www.who.int/ictrp/network/trds/en/index.html The date the final participant was examined or received an intervention for purposes of final collection of data for the primary and secondary outcome measures and adverse events (for example, last participant’s last visit), whether the clinical study concluded according to the pre-specified protocol or was terminated. https://prsinfo.clinicaltrials.gov/definitions.html completion date clinical trial study completion date completion date http://www.icmje.org/recommendations/ http://www.who.int/ictrp/network/trds/en/index.html The date that the final participant was examined or received an intervention for the purposes of final collection of data for the primary outcome, whether the clinical study concluded according to the pre-specified protocol or was terminated. In the case of clinical studies with more than one primary outcome measure with different completion dates, this term refers to the date on which data collection is completed for all of the primary outcomes. https://prsinfo.clinicaltrials.gov/definitions.html primary completion clinical trial primary completion date The main objective of the intervention(s) being evaluated by the clinical trial. primary purpose of clinical trial https://prsinfo.clinicaltrials.gov/definitions.html clinical trial primary purpose specification The date on which the study sponsor or investigator first submitted a study record to ClinicalTrials.gov. There is typically a delay of a few days between the first submitted date and the record's availability on ClinicalTrials.gov (the first posted date). a date when a registration occurs First submitted date of registration in primary registry date of registration The date on which the study sponsor or investigator first submitted a study record to ClinicalTrials.gov. There is typically a delay of a few days between the first submitted date and the record's availability on ClinicalTrials.gov (the first posted date). https://www.clinicaltrials.gov/ct2/about-studies/glossary date of registration in primary registry https://www.who.int/ictrp/network/trds/en/ The current stage of a clinical study and whether it is or will be open for enrollment The recruitment status for the clinical study as a whole, based upon the status of the individual sites. If at least one facility in a multi-site clinical study has an Individual Site Status of "Recruiting," then the Overall Recruitment Status for the study must be "Recruiting." Oliver He https://clinicaltrials.gov/ct2/help/glossary/recruitment-status recruitment status http://www.icmje.org/recommendations/ http://www.who.int/ictrp/network/trds/en/index.html The recruitment status for the clinical study as a whole, based upon the status of the individual sites. If at least one facility in a multi-site clinical study has an Individual Site Status of "Recruiting," then the Overall Recruitment Status for the study must be "Recruiting." https://prsinfo.clinicaltrials.gov/definitions.html Oliver He, Edison Ong status The current stage of a clinical study and whether it is or will be open for enrollment Oliver He https://clinicaltrials.gov/ct2/help/glossary/recruitment-status study status Qingliang Leon Li, Asiyah Yu Lin, Oliver He https://pubchem.ncbi.nlm.nih.gov/source/NIPH%20Clinical%20Trials%20Search%20of%20Japan https://rctportal.niph.go.jp/en/ Japan clinical trial identifier https://www.who.int/ictrp/network/jprn2/en/ A Japan clinical trial identifier provided by the University Hospital Medical Information Network Center (UMIN-CTR) Qingliang Leon Li, Asiyah Yu Lin, Oliver He UMIN https://rctportal.niph.go.jp/en/ UMIN-CTR clinical trial identifier Qingliang Leon Li, Asiyah Yu Lin, Oliver He JapicCTI https://rctportal.niph.go.jp/en/ JAPIC clinical trial identifier A centrally registered identifier that is assigned for a specific clinical trial registered in JMACCT. The format for the JMACCT registry number is “JMA-IIA” followed by a 5-digit number, e.g., JMA-IIA00391. Qingliang Leon Li, Asiyah Yu Lin, Oliver He JMACCT https://rctportal.niph.go.jp/en/ JMACCT clinical trial identifier EudraCT Number: 2007-002422-29 Qingliang Leon Li, Asiyah Yu Lin, Oliver He EudraCT identifier https://en.wikipedia.org/wiki/EudraCT https://www.clinicaltrialsregister.eu/ctr-search/search https://www.clinicaltrialsregister.eu/ctr-search/search?query=eudract European clinical trial registry identifier https://www.who.int/ictrp/network/primary/en/ Combining a drug and device, a biological product and device; a drug and biological product; or a drug, biological product, and device Leon Li, Asiyah Lin, Oliver He combinational intervention Combining a drug and device, a biological product and device; a drug and biological product; or a drug, biological product, and device https://prsinfo.clinicaltrials.gov/definitions.html The quality of a clinical trial that studies a drug or biological product. The phase is based on the study's objective, the number of participants, and other characteristics. According to USA FDA, there are five phases: Early Phase 1 (formerly listed as Phase 0), Phase 1, Phase 2, Phase 3, and Phase 4. Leon Li, Asiyah Lin, Oliver He clinical trial stage https://www.clinicaltrials.gov/ct2/help/glossary/phase phase clinical trial phase https://www.who.int/ictrp/network/trds/en/ A clinical trial phase that represents the first-in-man trial, which tests within a small group of people (typically 20-80) to evaluate safety, determine safe dosage ranges, and begin to identify side effects. A drug's side effects could be subtle or long term, or may only happen with a few people, so phase 1 trials are not expected to identify all side effects. Leon Li, Asiyah Lin, Oliver He Phase 1 Phase I http://purl.obolibrary.org/obo/NCIT_C15600 https://en.wikipedia.org/wiki/Clinical_trial C0920321 C15600 clinical trial phase 1 A clinical trial phase that is designed to study a biomedical or behavioral intervention in a larger group of people (several hundred), to evaluate the drug's effectiveness for a particular indication in patients with the disease or condition under study, and to determine the common short-term side effects and risks associated with the intervention. [def-source: NCI] Leon Li, Asiyah Lin, Oliver He Phase II http://purl.obolibrary.org/obo/NCIT_C15601 https://en.wikipedia.org/wiki/Clinical_trial C0282460 C15601 clinical trial phase 2 A clinical trial phase that is designed to investigate the efficacy of the biomedical or behavioral intervention in large groups of human subjects (from several hundred to several thousand), to confirm efficacy, to monitor adverse reactions to the new medication or treatment regimen with respect to long-term use and by comparing the intervention to other standard or experimental interventions as well as to a placebo. [def-source: NCI] Leon Li, Asiyah Lin, Oliver He Phase III http://purl.obolibrary.org/obo/NCIT_C15602 https://en.wikipedia.org/wiki/Clinical_trial C0282461 C15602 clinical trial phase 3 A clinical trial phase that is designed for a randomized, controlled trial to evaluate the long-term safety and efficacy of a drug for a given indication. Often they are designed to study side effects that may have become apparent after the phase III study was completed. [def-source: NCI] Leon Li, Asiyah Lin, Oliver He Phase IV https://en.wikipedia.org/wiki/Clinical_trial C0282462 C15603 clinical trial phase 4 A clinical trial phase that is designed to use an investigational agent that is available only in very limited quantities and which has never previously given to humans or for which there is extremely limited human experience. Phase 0 clinical trials are intended to enable researchers to understand the path of the drug in the body and its efficacy. Adverse event reporting in Phase 0 trials is expedited. [def-source: NCI] Leon Li, Asiyah Lin, Oliver He Early Phase 1 Pre-Clinical Phase clinical trial phase 0 http://purl.obolibrary.org/obo/NCIT_C54721 https://en.wikipedia.org/wiki/Clinical_trial C1882358 C54721 clinical trial early phase 1 A medical intervention that involves a behavioral process to control, prevent, or treat a behavior problem. Leon Li, Asiyah Lin, Oliver He https://www.understood.org/en/learning-attention-issues/treatments-approaches/educational-strategies/behavior-intervention-plans-what-you-need-to-know behavioral behavioral intervention behavioral https://prsinfo.clinicaltrials.gov/definitions.html human subject In clinicaltrials.gov, contact information character limits: First Name: 62 characters Last Name: 62 characters Degree: 30 characters Phone: 30 characters Phone Ext: 14 characters Email: 254 characters Citation: https://prsinfo.clinicaltrials.gov/definitions.html#StudyOfficials A person who serves as a contact role and has disclosed specified information to be reached. Usually the contact information, such as email and phone number, is provided., Leon, Asiyah, Oliver: Since each contact needs to provide some contact information, we may need to define the contact information. Leon Li, Asiyah Lin, Oliver He https://prsinfo.clinicaltrials.gov/definitions.html#StudyOfficials contact person A contact person for each facility participating in a study. Leon Li, Asiyah Lin, Oliver He https://prsinfo.clinicaltrials.gov/definitions.html facility contact Leon Li, Asiyah Lin, Oliver He https://prsinfo.clinicaltrials.gov/definitions.html#StudyOfficials contact of scientific queries An investigation agent role that is taken by a human individual Leon Li, Asiyah Lin, Oliver He human investigator role investigator role a role taken by a person who serves as a contact for some process. Leon Li, Asiyah Lin, Oliver He contact person role Leon Li, Asiyah Lin, Oliver He https://prsinfo.clinicaltrials.gov/definitions.html#StudyOfficials contact for public queries A person to whom questions concerning enrollment at any location of the study can be addressed. Leon Li, Asiyah Lin, Oliver He central contact person https://prsinfo.clinicaltrials.gov/definitions.html central contact person of study information content entity about a contact person Leon Li, Asiyah Lin, Oliver He contact person information A sponsor role taken by an individual, organization, group or other legal entity which takes responsibility for initiating, managing and/or financing a study. The Primary Sponsor is responsible for ensuring that the trial is properly registered. The Primary Sponsor may or may not be the main funder. Leon Li, Asiyah Lin, Oliver He https://www.who.int/ictrp/network/trds/en/ primary sponsor role A sponsor role taken by an additional individual, organization or another legal person, if any, that has agreed with the primary sponsor to take on responsibilities of sponsorship. Leon Li, Asiyah Lin, Oliver He collaborator role https://www.who.int/ictrp/network/trds/en/ A secondary sponsor may have agreed to: - take on all the responsibilities of sponsorship jointly with the primary sponsor; or - form a group with the Primary Sponsor in which the responsibilities of sponsorship are allocated among the members of the group; or - act as the Primary Sponsor’s legal representative in relation to some or all of the trial sites. by WHO (https://www.who.int/ictrp/network/trds/en/) In clinicaltrials.gov, the secondary sponsor role can be taken by a project collaborator (Reference: https://prsinfo.clinicaltrials.gov/trainTrainer/WHO-ICMJE-ClinTrialsgov-Cross-Ref.pdf). However, a secondary sponsor may serve as a collaborator role, but a collaborator may not serve as a secondary sponsor role. secondary sponsor role An investigator role taken by an individual who is designated as responsible party by the sponsor Leon Li, Asiyah Lin, Oliver He https://prsinfo.clinicaltrials.gov/definitions.html principal investigator role An investigator role taken by an individual who both initiates and conducts the study Leon Li, Asiyah Lin, Oliver He https://prsinfo.clinicaltrials.gov/definitions.html sponsor investigator role An investigation agent role taken by an agent (an individual, organization, group or another legal entity) who provides support to an investigation. The support may include funding, design, implementation, data analysis or reporting. The responsible party is responsible for confirming all collaborators before listing them. Leon Li, Asiyah Li, Oliver He collaborator role https://prsinfo.clinicaltrials.gov/definitions.html#Collaborators https://www.who.int/ictrp/network/trds/en/ A secondary sponsor may serve as a collaborator role. However, a collaborator may not serve as a secondary sponsor role. investigation collaborator role A systematic, scientific investigation that can be either interventional or observational and involves human beings as research subjects. Human subject research can be either medical (clinical) research or non-medical (e.g., social science) research. Oliver He human investigation human study https://en.wikipedia.org/wiki/Human_subject_research human subject study a clinical trial is a medical interventional study where participants are assigned prospectively to an intervention or interventions according to a protocol to evaluate the safety and efficacy of the intervention(s) on biomedical or other health related outcomes. The Interventions include but are not restricted to drugs, cells and other biological products, surgical procedures, radiologic procedures, devices, behavioral treatments, process-of-care changes, preventive care, etc. Oliver He, Asiyah Yu Lin, Qingliang Li interventional trial https://clinicaltrials.gov/ct2/search/map https://en.wikipedia.org/wiki/Clinical_trial https://prsinfo.clinicaltrials.gov/definitions.html https://www.who.int/ictrp/en/ clinical trial A clinical trial that is at Early Phase 1 or Phase 0 A clinical trial that is at an Early Phase i or Phase 0, which is designed to use an investigational agent that is available only in very limited quantities and which has never previously given to humans or for which there is extremely limited human experience. Phase 0 clinical trials are intended to enable researchers to understand the path of the drug in the body and its efficacy. Adverse event reporting in Phase 0 trials is expedited. [def-source: NCI] Exploratory trials, involving very limited human exposure, with no therapeutic or diagnostic intent (e.g., screening studies, microdose studies). (Formerly listed as "Phase 0") Leon Li, Asiyah Lin, Oliver He Phase 0 clinical trial Phase 0 trial Pre-Clinical Trial http://purl.obolibrary.org/obo/NCIT_C54721 https://en.wikipedia.org/wiki/Clinical_trial Early Phase 1 clinical trial Exploratory trials, involving very limited human exposure, with no therapeutic or diagnostic intent (e.g., screening studies, microdose studies). (Formerly listed as "Phase 0") https://prsinfo.clinicaltrials.gov/definitions.html An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. quality PATO:0000047 biological sex A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. quality PATO:0000383 female A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. quality PATO:0000384 male A quality which inheres in an process. PATO:0001239 PATO:0001240 quality of a process quality of occurrent quality of process relational quality of occurrent quality PATO:0001236 See comments of relational quality of a physical entity. process quality A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. quality PATO:0001894 phenotypic sex A quality that inheres in an entire organism or part of an organism. quality PATO:0001995 organismal quality An information content entity that describes some relationships between some entities and whose truthfullness is a prerequisite for something. Une entité de contenu informationnel qui décrit des relations entre certaines entités et dont la véracité est un prérequis pour quelque chose. condition condition a medical intervention that involves in adding vaccine into a host (e.g., human, mouse) in vivo with the intent to invoke an adaptive immune response. vaccination https://prsinfo.clinicaltrials.gov/definitions.html A vaccine clinical trial that investigates the safety profile of a vaccine in a small group (10-50) of healthy volunteers. YH phase 1 vaccine trial A vaccine clinical trial that studies vaccine efficacy with a target population (numbering 50-100). Different dosage levels will also be explored at this stage to determine the optimum dose. YH phase 2 vaccine trial A vaccine clinical trial that takes the trial to a large-scale safety and efficacy study in a relevant patient population, usually in excess of 3,000. YH phase 3 vaccine trial The final stage of vaccine clinical evaluation. Phase IV occurs after a vaccine or therapy is licensed and is being used by large numbers of people. These studies are not always required or completed. YH phase 4 vaccine trial A processual entity by which a vaccine is tested clinically for safety and effectiveness. Clinical trials are conducted in phases. Classically, clinical trials unfold in three phases in order to gather data and information about a vaccine and its performance. This will form the basis of a dossier submitted to regulatory authorities by way of an application for licensure. After a vaccine is licensed and is being used by large numbers of people, a Phase IV study may or may not be taken for vaccine clinical evaluation. Most vaccines against a pathogen (e.g., HIV) are not tested by vaccinating people and then deliberately exposing them to virulent pathogen (e.g., HIV). This strategy is never for a vaccine against a disease as serious as HIV. The best way to determine if a vaccine is effective is to test it in a randomized, controlled, double-blind clinical trial. This type of trial is often referred to as the gold standard in medical research and provides the strongest evidence for the efficacy of a vaccine. YH vaccine clinical trial ready for release metadata incomplete pending final vetting single group of individuals with specific characteristics. single group of individuals with specific characteristics. https://prsinfo.clinicaltrials.gov/definitions.html The Ontology of Medically Related Social Entities Group of individuals with specific characteristics (for example, conditions or exposures) compared to group(s) with different characteristics, but otherwise similar. Group of individuals with specific characteristics (for example, conditions or exposures) compared to group(s) with different characteristics, but otherwise similar. https://prsinfo.clinicaltrials.gov/definitions.html Characteristics of case immediately prior to disease onset (sometimes called the hazard period) compared to characteristics of same case at a prior time (that is, control period). Characteristics of case immediately prior to disease onset (sometimes called the hazard period) compared to characteristics of same case at a prior time (that is, control period). https://prsinfo.clinicaltrials.gov/definitions.html Group of individuals, initially defined and composed, with common characteristics (for example, condition, birth year), who are examined or traced over a given time period. Group of individuals, initially defined and composed, with common characteristics (for example, condition, birth year), who are examined or traced over a given time period. https://prsinfo.clinicaltrials.gov/definitions.html Participants are assigned to one of two or more groups in parallel for the duration of the study Participants are assigned to one of two or more groups in parallel for the duration of the study https://prsinfo.clinicaltrials.gov/definitions.html Participants receive one of two (or more) alternative interventions during the initial phase of the study and receive the other intervention during the second phase of the study Participants receive one of two (or more) alternative interventions during the initial phase of the study and receive the other intervention during the second phase of the study https://prsinfo.clinicaltrials.gov/definitions.html Clinical trials with a single arm Clinical trials with a single arm https://prsinfo.clinicaltrials.gov/definitions.html Korean clinical trial registry identifier A centrally registered identifier that is assigned for a specific clinical trial registered in the Korean Clinical Research Information Service (CRIS). The format for the registry number is “KCT” followed by a 7-digit number, e.g., KCT0004537. CRIS identifier http://cris.nih.go.kr/cris/en/use_guide/cris_introduce.jsp Sri Lanka clinical trials registry identifier https://slctr.lk/ SLCTR identifier A centrally registered identifier that is assigned for a specific clinical trial registered in the Sri Lanka clinical trials registry (SLCTR ). The format for the registry number is “SLCTR /” followed by a 4-digit number, followed by a slash, followed a 3-digit number, e.g., SLCTR/2020/010 jRTC clinical trials register https://rctportal.niph.go.jp/en/ The jRTC (Japan Registry of Clinical Trials) clinical trial registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. Japan Registry of Clinical Trials https://jrct.niph.go.jp/ jRTC The international standard randomised controlled trial register is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials. http://www.isrctn.com/ ISRCTN International standard randomised controlled trial register