Amanda Hicks John Levander Josh Hanna Matt Diller Mike Wagner Shawn T. Brown William R. Hogan Mathias Brochhausen https://orcid.org/0000-0002-9881-1017 An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. https://creativecommons.org/licenses/by/4.0/ Apollo Structured Vocabulary (Apollo-SV) C87985BA-6A8A-483A-A6B6-63975101F672 082D5D78-D916-457E-B4FD-365F86F45B30 When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI). 2024-12-24 National Library of Medicine Identifier This identifier is the one that the National Library of Medicine uses to identify journals uniquely in PubMed. NLM ID linking ISSN International Standard Serial Number, Linking The linking ISSN is a single number assigned to all formats of a journal. The online and print versions of a journal, for example, are typically different. The linking ISSN refers to the journal regardless of format. ISSN Linking Iso Abbr ISO Abbreviations are constructed at NLM to assist NCBI in linking from GenBank to PubMed. ISO Title Abbreviation The abbreviated journal title assigned by the National Library of Medicine. Typically, it's the ISO title abbreviation without periods. NLM Title Abbreviation The date on which a URI annotated with this property was created. William R. Hogan This is the date that you created the URI that represents something, NOT the date that the thing referenced by the URI was created. For example, if you create a URI on 2014-09-24 to represent a book published on 1982-10-17, then this annotation property should have the value 2014-09-24. In other words, this annotation refers to the representation, not the represented thing. For the 1982-10-17 date, we suggest the dc:created annotation. URI creation date author list William R. Hogan an annotation property for capturing the list of authors on the publication or other document to which the entity to which the annotation is attached refers. That is, this annotation should be attached only to individuals that represent information content entities, and its values must denote the people that authored the ICE. author list <annotation> source code version control repository URL WIlliam R. Hogan This annotation is intended for annotating instances of software application, software module, ontology (artifact), etc. with a uniform resource locator that points to the source code version control repository where they are managed. Note that for OWL individuals that reference a particular version of the software or ontology, this URL should point to the place in the repository where that version is located, rather than the general main page of the repository. source code repository URL human readable synopsis A comment that summarizes the most relevant or salient features and history of the entity for human readers. William R. Hogan human readable synopsis Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label VIVO-ISF There are several URL and hasURL annotation properties out there in the ontology world. This one had the most sensible source ontology and OBO ID URI combination out there. hasURL US State Two Digit Identifier US State Two Letter Abbreviation US State Ens Identifier UN Numerical Code ISO 3166-1-alpha-3 code ISO 3166-1-alpha-2 code Proposed Apollo Location Code ISO 3166-2 code geonameid integer id of record in geonames database geonameid geonames admin1 code fipscode (subject to change to iso code), see exceptions below, see file admin1Codes.txt for display names of this code; varchar(20) admin1 code geonames admin2 code code for the second administrative division, a county in the US, see file admin2Codes.txt; varchar(80) admin2 code geonames admin3 code code for third level administrative division, varchar(20) admin3 code geonames admin4 code code for fourth level administrative division, varchar(20) admin4 code editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status definition 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 textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor definition editor term editor alternative label alternative term A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label alternative term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note 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 ontology term requester The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester is denotator type Relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg is denotator type 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 expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall Chris Mungall expand expression to expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property part_of antisymmetric property xsd:true Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label has ID digit count Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) Person:Alan Ruttenberg has ID digit count has ID range allocated Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID range allocated to has ID policy for Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for has ID prefix Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. Person:Alan Ruttenberg has ID prefix elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) is allocated id range Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg Add as annotation triples in the granting ontology is allocated id range retired from use as of relates a class of CRID to the date after which further instances should not be made, according to the central authority In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp Alan Ruttenberg retired from use as of has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. Nicolas Matentzoglu has ontology root term may be identical to A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. David Osumi-Sutherland #40 VFB Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to scheduled for obsoletion on or after Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. Chris Mungall, Jie Zheng https://github.com/geneontology/go-ontology/issues/15532 https://github.com/information-artifact-ontology/ontology-metadata/issues/32 GO ontology scheduled for obsoletion on or after has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by ISA alternative term NIAID GSCID-BRC alternative term This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. OBO Operations call logical characteristic of object property 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. defined by construct An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive an alternative term used for STATO statistical ontology and ISA team Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra STATO alternative term external_definition homology_notes This annotation property gives the unique label of all Apollo_SV entities that are refered to in the schema. The UAL is the denotator for the Apollo_SV class in the schema. There can at all times only be ONE value of UAL for each class. UAL Unique Apollo Label A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored has_rank eco subset Creator Source Source dc:type has_alternative_id An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 database_cross_reference has_definition An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has_obo_namespace An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has_synonym_type id in_subset shorthand ontology instance unique identifier ontology IUI ontology version instance unique identifier ontology version IUI label label basis of true p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption. obsolete is based on true a commissions b, iff a does not participate in the creation or execution of b and participates in a legal agreement that c participates on the creation or execution of b and c getting something in exchange for that participation. A relation between two entities where the first entity formally requests a third party to create or execute the second entity. commissions commissions A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times. Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222. instantiates a simulates b, iff a is a purely intentional entity that is representing a fictional individual or fact b and a participates in a simulating. simulates Mathias Brochhausen causally_precedes true obsoleted_administrated by true has basis in quality (Q is_a Quality ⋀ D is_a Disposition ⋀ Q base of D) ® ∀q (q instance_of Q ® b (q inheres_in b ⋀ d (d instance_of D ⋀ d inheres_in b))) Representing dispositions Johannes Röhl and Ludger Jansen Journal of Biomedical Semantics 2011 2(Suppl 4):S4 DOI: 10.1186/2041-1480-2-S4-S4 The relationship between a disposition and the quality that confers the disposition on the material entity in which they both inhere. For example, the disposition of a piece of glass to bend light and the lattice structure of the glass (quality) that results in the bending of the light. has basis in is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 external part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of https://wiki.geneontology.org/Part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part BFO:0000051 external has_part has_part has part has part BFO_0000054 BFO_0000054s BFO_0000054ed obsolete_is_realized_by realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm] replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by' GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall executed_during has_realization is realized by is_realized_as realized by realized_by realized_in http://purl.obolibrary.org/obo/obi.owl [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process is realized by realized in BFO_0000055 BFO_0000055s BFO_0000055ed realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://purl.obolibrary.org/obo/ro.owl http://www.obofoundry.org/ro/#OBO_REL:preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. http://purl.obolibrary.org/obo/ro.owl precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in http://purl.obolibrary.org/obo/ido.owl http://purl.obolibrary.org/obo/obi.owl BFO:0000066 external relationship occurs_in occurs_in Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in occurs in unfolds_in https://wiki.geneontology.org/Occurs_in contains-process containsProcess site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t [XXX-001 http://purl.obolibrary.org/obo/bfo.owl Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process is aggregate of aggregate of aggregate_of http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/omrse.owl is aggregate of located-at-r_st occupiesSpatialRegionAt Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t) BFO2 Reference: independent continuant BFO2 Reference: spatial region b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002]) if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001]) (forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002] (forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002] (forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001] occupies spatial region at some time exists at BFO_0000110 BFO_0000110s BFO_0000110ed c-has-part_at hasContinuantPartAt [copied from inverse property 'part of continuant at all times that whole exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t) b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'. [copied from inverse property 'part of continuant at all times that whole exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times' http://purl.obolibrary.org/obo/bfo.owl (iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001] has continuant part at all times BFO_0000111 BFO_0000111s BFO_0000111ed c-has-ppart_at hasProperContinuantPartAt b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001 Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has proper continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has proper continuant part@en(x,y,t)'. http://purl.obolibrary.org/obo/bfo.owl has proper continuant part at all times has-material-basis_at hasMaterialBasisAt the material basis of John’s disposition to cough is the viral infection in John’s upper respiratory tract the material basis of the disposition to wear unevenly of John’s tires is the worn suspension of his car. Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has material basis at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has material basis@en(x,y,t)'. http://purl.obolibrary.org/obo/bfo.owl b has_material_basis c at t means: b is a disposition & c is a material entity & there is some d bearer_of b at t& c continuant_part_of d at t& d has_disposition b at t because c continuant_part_of d at t. (axiom label in BFO2 Reference: [071-002]) (forall (x y t) (if (hasMaterialBasisAt x y t) (and (Disposition x) (MaterialEntity y) (exists (z) (and (bearerOfAt z x t) (continuantPartOfAt y z t) (exists (w) (and (Disposition w) (if (hasDisposition z w) (continuantPartOfAt y z t))))))))) // axiom label in BFO2 CLIF: [071-002] has material basis at all times BFO_0000117 BFO_0000117s BFO_0000117ed o-has-part hasOccurrentPart [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life [copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match. b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent http://purl.obolibrary.org/obo/bfo.owl [copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] has occurrent part BFO_0000118 BFO_0000118s BFO_0000118ed o-has-ppart hasProperOccurrentPart [copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001]) b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001 http://purl.obolibrary.org/obo/bfo.owl has proper occurrent part has-t-part [copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life [copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life. [copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating [copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) [copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003]) http://purl.obolibrary.org/obo/bfo.owl has temporal part r-location-of_st [copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t) [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region [copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) has spatial occupant at some time BFO_0000132 BFO_0000132s BFO_0000132ed o-part-of occurrentPartOf Mary’s 5th birthday occurrent_part_of Mary’s life The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. the first set of the tennis match occurrent_part_of the tennis match. [copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. BFO2 Reference: occurrent http://purl.obolibrary.org/obo/bfo.owl b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001]) occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002]) occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001]) occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001]) occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001]) (forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001] (forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001] (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001] (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] part of occurrent t-ppart-of properTemporalPartOf http://purl.obolibrary.org/obo/bfo.owl proper temporal part of c-ppart-of_at properContinuantPartOfAt b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'proper part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'proper part of continuant@en(x,y,t)'. http://purl.obolibrary.org/obo/bfo.owl (iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001] proper part of continuant at all times o-ppart-of properOccurrentPartOf [copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001 b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001]) http://purl.obolibrary.org/obo/bfo.owl (iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001] proper part of occurrent t-part-of temporalPartOf the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life the process boundary which separates the 3rd and 4th years of your life. your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003]) http://purl.obolibrary.org/obo/bfo.owl if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002]) (forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002] (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001] (iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003] temporal part of spans occupiesTemporalRegion http://purl.obolibrary.org/obo/bfo.owl p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) occupies temporal region span-of spanOf http://purl.obolibrary.org/obo/bfo.owl [copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) has temporal occupant during which exists BFO_0000167 BFO_0000167s BFO_0000167ed has participant at all times specificallyDependsOn A pain s-depends_on the organism that is experiencing the pain a gait s-depends_on the walking object. (All at some specific time.) a shape s-depends_on the shaped object one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs reciprocal s-dependence between occurrents: a process of buying and the associated process of selling reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball the one-sided dependence of an occurrent on an independent continuant: handwave on a hand the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45 the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45 the two-sided reciprocal s-dependence of the roles of husband and wife [20 Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t) BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28 BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20 BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place. BFO2 Reference: specifically dependent continuant\; process; process boundary To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64 If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001]) If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001]) If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002]) an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002]) if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002]) (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002] (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002] (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001] (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002] (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] specifically depends on at some time c-part-of_at continuantPartOfAt Mary’s arm continuant_part_of Mary in the time of her life prior to her operation the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. [copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'. BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. BFO2 Reference: continuant BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. [copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times' http://purl.obolibrary.org/obo/bfo.owl b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001]) continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002]) continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001]) continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001]) continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001]) if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002]) (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] (forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] part of continuant at all times has-t-ppart http://purl.obolibrary.org/obo/bfo.owl has proper temporal part history of has history c-has-part-object_at [copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation [copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t) This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times' [copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'. [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. http://purl.obolibrary.org/obo/bfo.owl [copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) has continuant part at all times that part exists is in aggregate A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1's jurisdiction falls within the relevant jurisdiction of G2. 'is subordinate authority of' Domain: governing organization Range: governing organization Formal properties: transitive, anti-symmetric, irreflexive Natural language definition: A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1 falls within the relevant jurisdiction of G2. is subordinate authority of It is not intended to be maximal, in the sense that if a has_jurisdiction_in b, and b is not part of c, then a NOT has_jurisdiction_in c. in other words, it is perfectly fine to say: a disjoint b c has_jurisdiction_in a c has_jurisdiction_in b otherwise, we'd end up creating some mereological sum of all the islands, contiguous land masses, etc. of the United States, calling it "United States territory", asserting United States has_jurisdiction_in United States territory, then figuring out all the parts of that territory like islands, etc. We'd end up doing the same thing for every sovereign state, major administrative subdivision (at least those like Hawaii that are multiple), etc. Seems like an unnecessary duplication of entities. a governmental organization has jurisdiction in particular territories (areas of land), which means that it can make and enforce laws that govern peoples living in those territories. if a has_jurisdiction_in b, then a has_jurisdiction_in all parts of b. has jurisdiction in has measurement unit label A relation between a value specification and its unit of measurement. http://purl.obolibrary.org/obo/obi.owl has measurement unit label The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file. 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy obsolete_specifically denotes true This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy http://purl.obolibrary.org/obo/iao.owl is about An information artifact IA mentions an entity E exactly when it has a component/part that denotes E 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition PERSON: Jonathan Rees Person: Alan Ruttenberg mentions Inverse of the relation 'mentions' 2022-01-28T07:20:08Z mentioned by A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote obsolete_materially denotes true m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes. From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input. This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. Alan Ruttenberg is quality measurement of obsolete_describes true obsolete_represents true inverse of the relation 'denotes' Person: Jie Zheng, Chris Stoeckert, Mike Conlon denoted by relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point has coordinate unit label relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of inverse of the relation of is quality measurement of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg is quality measured as A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. Person:Alan Ruttenberg Person:Bjoern Peters is quality specification of inverse of the relation of is quality specification of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg Person:Bjoern Peters quality is specified as relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken Alan Ruttenberg has time stamp relates a time stamped measurement datum to the measurement datum that was measured Alan Ruttenberg has measurement datum results_in Mathias Brochhausen This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal. owns a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b. Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. is owned by has_specified_input has_specified_input see is_input_of example_of_usage The inverse property of is_specified_input_of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot http://purl.obolibrary.org/obo/obi.owl has_specified_input is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay Alan Ruttenberg PERSON:Bjoern Peters http://purl.obolibrary.org/obo/obi.owl is_specified_input_of has_specified_output has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot http://purl.obolibrary.org/obo/obi.owl has_specified_output true is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters http://purl.obolibrary.org/obo/obi.owl is_specified_output_of is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch http://purl.obolibrary.org/obo/obi.owl achieves_planned_objective has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI http://purl.obolibrary.org/obo/obi.owl has value specification Mathias Brochhausen Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. http://purl.obolibrary.org/obo/omrse.owl This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal. obsolete owns owns true a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b. Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. Reinach, A. S�mtliche Werke. Texkritische Ausgabe, M�nchen: Philosophia Verlag, 1989, p.189-204. http://purl.obolibrary.org/obo/omrse.owl is owned by obsolete is owned by is administered by is enrolled in school is admitted to hospital inheres in this fragility inheres in this vase this fragility is a characteristic of this vase this red color inheres in this apple this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer of bearer_of is bearer of http://purl.obolibrary.org/obo/omrse.owl bearer of bearer_of has characteristic is bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in http://purl.obolibrary.org/obo/obi.owl participates in has participant has_participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://purl.obolibrary.org/obo/obi.owl http://www.obofoundry.org/ro/#OBO_REL:has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant has_participant has_participant is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. http://purl.obolibrary.org/obo/obi.owl is concretized as concretizes is_concretization_of A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. http://purl.obolibrary.org/obo/obi.owl concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime location_of location of located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime located_in http://www.obofoundry.org/ro/#OBO_REL:located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in https://wiki.geneontology.org/Located_in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of 2D boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary has 2D boundary A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. 2017-05-24T09:49:21Z has component process 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. David Osumi-Sutherland Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which ends David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) David Osumi-Sutherland starts_at_end_of http://purl.obolibrary.org/obo/uberon.owl A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 http://semanticscience.org/resource/SIO_000251 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately_preceded_by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes immediately_precedes David Osumi-Sutherland o overlaps RO:0002093 external ends_during ends_during X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during ends during x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps true A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 external regulates regulates regulates regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y Chris Mungall http://purl.obolibrary.org/obo/ro.owl negatively regulates (process to process) RO:0002212 external negatively_regulates negatively_regulates negatively regulates negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. positively regulates (process to process) RO:0002213 external positively_regulates positively_regulates positively regulates positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. has function in capable of part of true 'heart development' has active participant some Shh protein OBSOLETE x has participant y if and only if x realizes some active role that inheres in y x has participant y if and only if x realizes some active role that inheres in y This may be obsoleted and replaced by the original 'has agent' relation Chris Mungall has agent http://purl.obolibrary.org/obo/ro.owl has active participant obsolete has active participant true A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO Chris Mungall http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl adjacent to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. move to BFO? Allen Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. http://purl.obolibrary.org/obo/obi.owl https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporal relation temporally related to inverse of starts with Chris Mungall Allen starts Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by http://purl.obolibrary.org/obo/obi.owl starts with inverse of ends with inverse of ends with Chris Mungall http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl ends x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by finished with http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl ends with x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y starts with process that occurs in has start location x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y ends with process that occurs in has end location p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. consumes has input https://wiki.geneontology.org/Has_input p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. Chris Mungall produces has output https://wiki.geneontology.org/Has_output A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within https://wiki.geneontology.org/Acts_upstream_of_or_within an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) Chris Mungall GOC:mtg_berkeley_2013 results_in_formation_of results in formation of p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. causally upstream of, negative effect q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of inheres in part of characteristic of part of true A mereological relationship or a topological relationship Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. Chris Mungall http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl Gene Ontology Consortium colocalizes with a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables https://wiki.geneontology.org/Enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. false part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p actively involved in enables part of involved in https://wiki.geneontology.org/Involved_in inverse of enables enabled by https://wiki.geneontology.org/Enabled_by inverse of regulates regulated by (processual) regulated by inverse of negatively regulates negatively regulated by inverse of positively regulates positively regulated by An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member inverse of has input input of inverse of has output output of A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with inverse of upstream of Chris Mungall http://purl.obolibrary.org/obo/ro.owl causally downstream of immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. indirectly activates indirectly positively regulates https://wiki.geneontology.org/Indirectly_positively_regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly inhibits indirectly negatively regulates https://wiki.geneontology.org/Indirectly_negatively_regulates relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. https://en.wikipedia.org/wiki/Causality p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall http://purl.obolibrary.org/obo/ro.owl causally upstream of p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. immediately causally upstream of p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 influences (processual) affects causally upstream of or within inverse of causally upstream of or within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. executes activity in enables activity in is active in https://wiki.geneontology.org/Is_active_in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. A relationship that holds between two entities in which the processes executed by the two entities are causally connected. This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Considering relabeling as 'pairwise interacts with' Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. molecularly controls directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. directly inhibits molecularly decreases activity of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. directly activates molecularly increases activity of directly positively regulates activity of This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. has part that occurs in true is kinase activity A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. http://purl.obolibrary.org/obo/ro.owl causal relation between processes depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities causally influenced by (entity-centric) causally influenced by interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ molecular interaction relation helper property The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). causally influences (entity-centric) causally influences p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) directly positively regulates https://wiki.geneontology.org/Directly_positively_regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) directly negatively regulates https://wiki.geneontology.org/Directly_negatively_regulates a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces a produced_by b iff some process that occurs_in b has_output a. produced by A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. 2017-12-26T19:45:49Z realized in response to stimulus Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. 2018-01-25T23:20:13Z enables subfunction 2018-01-26T23:49:30Z acts upstream of or within, positive effect https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect 2018-01-26T23:49:51Z acts upstream of or within, negative effect https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive 2018-01-26T23:53:14Z acts upstream of, positive effect https://wiki.geneontology.org/Acts_upstream_of,_positive_effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative 2018-01-26T23:53:22Z acts upstream of, negative effect https://wiki.geneontology.org/Acts_upstream_of,_negative_effect 2018-03-13T23:55:05Z causally upstream of or within, negative effect https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect 2018-03-13T23:55:19Z causally upstream of or within, positive effect DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. DEPRECATED inheres in true DEPRECATED bearer of true A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. triggered by process realized in response to https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit triggered by process Genetic information generically depend on molecules of DNA. The novel *War and Peace* generically depends on this copy of the novel. The pattern shared by chess boards generically depends on any chess board. The score of a symphony g-depends on a copy of the score. This pdf file generically depends on this server. A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. [072-ISO] g-depends on generically depends on Molecules of DNA are carriers of genetic information. This copy of *War and Peace* is carrier of the novel written by Tolstoy. This hard drive is carrier of these data items. *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* [072-ISO] is carrier of The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. regulates activity of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. 2022-09-26T06:07:17Z indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. 2022-09-26T06:08:01Z indirectly regulates A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. negatively regulates characteristic http://purl.obolibrary.org/obo/ido.owl relationship obsolete has_disposition true http://purl.obolibrary.org/obo/ido.owl relationship negatively_regulates true http://purl.obolibrary.org/obo/ido.owl OBO_REL:0000035 OBO_REL:realized_as relationship NOTE: there appears to be some consistency in usage as to whether processes or continuants realize obsolete_realized_by true http://purl.obolibrary.org/obo/ido.owl relationship regulates true ObsoleteProperty true obsolete has proper part true true true true a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred from c to a. A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl is expressed as A relation between a scalar measurement data item and a number that quantifies it. The range should probably not be restricted to "float". It makes sense to set it to "real". However we do not know how this change will affect SPARQL queries, so we have left the range as-is for now. http://purl.obolibrary.org/obo/obi.owl has measurement value has x coordinate value has z coordinate value has y coordinate value Stegomyia albopicta forest day mosquito Aedes albopictus A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an "act") that is laden with determinate, uniformily structured content. A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an "act") that is laden with determinate, uniformily structured content. Ingarden, R. (1964) Der Streit um die Existenz der Welt I. Existentalontologie. Max Niemeyer, Tübingen. Ingarden, R. (1965a) Das literarische Kunstwerk. 3. Auflage. Max Niemeyer, Tübingen. Ingarden, R. (1965b) Der Streit um die Existenz der Welt II/1. Formalontologie 1. Teil. Max Niemeyer, Tübingen. Johansson I. (2009) Proof of the existence of universals – and Roman Ingarden's Ontology. Metaphysica. International Journal for Ontology & Metaphysics. 10, 65-87 Thomasson AL. "Ingarden and the Ontology of Cultural Objects." In: Chrudziminski A (ed.): Existence, Culture, and Person. The Ontology of Roman Ingarden. Frankfurt: ontos, 2005, 115-136. MB: Right now we represent 'purely intentional entities' as siblings to 'information content entities'. Given their nature I am not entirly sure that this is correct. It seems that both 'information content entity' and 'simulation' are subclass to 'purely intentional entity'. purely intentional entity A disease transmission model whose concretization is realized as a simulation of infectious disease epidemic or infectious disease pandemic. William Hogan and Michael Wagner An algorithm the concretizations of which models the transmission of transmissible disease. epidemic model The average number of transmissions of an infectious agent from an infectious organism to a susceptible organism within a completely susceptible population. William R. Hogan The number of organisms that each infected organism infects in a completely susceptible population during its infectious period. basicReproductionNumbers MB: Here we run into the well know DL problem that we cannot specify that the infectious agent that is transmitted is of the same type that the infectious agent the population is susceptible to. basic reproduction number A population survey that assesses the level of immunity against a particular pathogen in a specified population. Mathias Brochhausen A population survey that assesses the level of immunity against a particular pathogen in a specified population. Comment from Mike (to do!): I checked because an infection and immunity census would involve two different census methods. One would be some kind of disease surveillance that counts infections. The other is some kind of immunity census process based on seroprevalence studies or vaccination registries. population immunity survey a planned process that (1) has at least one process part that has as participants representations of participants (in place of those participants) of processes of type X, and where all such process parts substitute for parts of processes of type X, and (2) is carried out for the purpose of planning for processes of type X, learning more about processes of type X, or teaching about processes of type X. A process that replaces the essential participants of another type of process with representations of those participants. simulating of process of type X For example, in a simulated volcano eruption, representations of lava, lava tubes, vents, etc. take the place of actual lava, lava tubes, vents, etc. Even in the case of a simulated disaster scenario where actual ambulances, fire trucks, and people participate, representations of catastrophic events and injuries, etc. take the place of real ones. simulating of process of type X An identifier that refers to the legal person that commissions a simulation process. An identifier that refers to the person or organization who is requesting one or more executions of the simulator software. Class was originally created to correspond with a complex type from Apollo XSD v3.1.0. simulation requester identifier A software application that provides a model of a real phenomenon based on a set of mathematical formulas. http://en.wikipedia.org/wiki/Simulation_software A software application that provides a model of a real phenomenon based on a set of mathematical formulas. simulator simulation software application A planned process that has specified output a software product and that involves the creation of source code. Mathias Brochhausen William R. Hogan http://en.wikipedia.org/wiki/Software_development A planned process resulting in a software product involving the creation of source code. software development An identifier that refers to the legal person that creates and maintains a simulator. An identifier that refers to the person or organization who is responsible for the simulator. It is intended to uniquely identify a person or organization. That said, we do not plan to control the namespace for simulator developer at this point in development. We will add our ideas about alternatives at a future date. simulator developer identifier An identifier that refers to all version of a specific simulator. An identifier that refers to all versions of a specific simulator, such as “FRED”. We intend that it uniquely identify a simulator when combined with simulator developer. For example, the combination www.psc.edu/FRED would differentiate the FRED simulator created by a Pittsburgh organization from another “FRED” simulator maintained elsewhere. The implementation of namespace control for simulator name (i.e., making sure that they don’t use “FRED” twice) is the responsibility of simulator developer. simulator identifier A control strategy start time information item that is based on a condition that triggers the control strategy. Mathias Brochhausen A control strategy start time information item that is based on a condition that triggers the control strategy. control strategy reactive start time information true A numeral that is part of a simulation time step action specification. A number of time step units in a time step of a simulation. For example, if the time step is 6 hours, then this value is 6. numberOfUnitsOfTimeInOneSimulatorStep simulation time step value An identifier that, as part of a complete simulator identifier, refers to one specific version of a simulator software. An identifier that refers to a unique version of a simulator. Simulator version distinguishes, for example, version “2.0” from “2.0.b” simulator version identifier A time unit that is part of a simulation time step action specification. A unit of time for each time step of a simulation, such as “hours” or “days”. unitOfTimeForSimulatorTimeStep simulation time step unit The action specification that specifies the number of time steps a simulation is going to run. The number of time steps in a simulator run. For example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero. runLength simulation run length A duration of the parts of an infection during which the host bears an infectious disposition in a population of hosts. Mathias Brochhausen A period when an individual of a particular species, who is infected with a particular pathogen, is able to infect susceptible organisms of a particular species. Note that the susceptible and infectious organisms can be of different species. infectiousPeriodDuration MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs. infectious period duration A duration of the time interval between the host acquiring an infection and the host bearing a contagiousness disposition during the same disease course within a population of hosts. Mathias Brochhausen A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species. Note that the susceptible and infected organisms can be of different species. latentPeriodDuration MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs The duration of the period between when an organism becomes infected and when it becomes infectious. latent period duration Mathias Brochhausen count of simulated susceptible population Mathias Brochhausen count of simulated exposed population Mathias Brochhausen count of simulated contagious population Mathias Brochhausen count of simulated resistant population The count of (simulated organisms) in a simulated population. Mathias Brochhausen The number of simulated organisms in a simulated population. The number does not have to be an integer. MW: I know this causes problems with our set-theoretic definition. Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step. Any ideas? I’ve considered and rejected allowing individual organisms to be fractional. Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’ count of simulated population An action specification comprising the number of doses and their timing for a vaccination of an individual organism against a specific infectious agent. A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism. vaccination dose schedule The fraction expressing the probability that an organism who is eligible according to a particular vaccination policy will be consented for that vaccination. The fraction of individuals in a population who are eligible according to a particular vaccination policy and will accept vaccination assuming no supply constraint. MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class "eligibility rule" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly. MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy” and “control measure efficacy delay.” We could then post-coordinate particular control measures such as vaccine. It is worth noting that there are control measures such as closing schools that are not applied at the individual level. We have not represented those control measures yet. vaccination compliance The infectious disease treatment efficacy of a vaccine. The degree to which a particular vaccination reduces the probability that a vaccinated individual will have a particular vaccination preventable outcome. vaccinationEfficacies Notes: 1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’ 2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer need to generate class restriction. Something like: 'is realized by' some (processual_entity and (has_participant some ('Anatomical structure' and ('is physical basis of' some 'protective resistance')) we'd also like to say that the protective resistance disposition began to exist during the process. can't recall whether we should use process or processual_entity for future BFO compatibility. vaccination efficacy A planned process involving counting numbers of facilities in a specific region. A planned process involving counting numbers of facilities in a specific region. facility survey Mathias Brochhausen Motivating use case is Synthia synthetic population data. school facility census A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease. A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease. infectious disease control strategy execution 1 Mathias Brochhausen Key motivating use case was Synthia synthetic population data. hospital patient population A simulation of a population or populations of organisms of a particular biological taxon that simulates a particular type of event or types of event that occur in a specified time interval. Mathias Brochhausen A simulated population is a set of simulated organisms. The set can be null (e.g., the set of 200 year-old H. sapiens). A simulated population can include more than one species, in which case it may be convenient to define each species as a simulated population and form the overall simulated population by set union. Similarly, it may be convenient to define sociodemographic or geographic strata within a simulated population as simulated populations and obtain the overall simulated population by set union. See examples in “Programmer’s Guide, page x) simulatorReferencablePopulation simulated population A measurement datum that is the output of counting. Mathias Brochhausen A measurement datum that is the output of counting. count count The planned process of finding the number of elements in a finite set of objects. Mathias Brochhausen http://en.wikipedia.org/wiki/Counting The planned process of finding the number of elements in a finite set of objects. counting a simulation that is about an organism simulation of organism A continuous parametric probability distribution that is uniform; centered around the mean, parameter μ​; and whose spread of standard deviations, parameter σ​, adheres to the empirical rule. A continuous probability distribution in which the parameter μ is the mean or expectation of the distribution and the parameter σ is its standard deviation NormalDistribution normal distribution A simulation of an infectious agent host that is not contagious and is part of a simulated population. A simulated organism in a simulated population that has acquired a particular simulated disease but is not yet able to transmit the disease to another simulated organism. simulation of exposed organism An identifier that refers to a geographical location to be used as location of a population in a simulation. Mathias Brochhausen An identifier referring to geographical location of a simulated population. Our intent is for the location identifiers to be INCITS codes. simulated population location identifier A simulation of an infectious organism host that is contagious. A simulated organism in a simulated population that has acquired a particular simulated disease and is able to transmit the disease to another simulated organism. simulation of infectious organism A simulated organism in a simulated population that is not susceptible. A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. Note that the name for this concept, were it to be named based on its intent, would be ‘immune.’ However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’ The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage. simulation of recovered organism A representation of a disposition realized in a represented disease course that at least part of the simulated population is represented as participating in. Mathias Brochhausen The disease being simulated. disease simulation of disease The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection. Mathias Brochhausen The number of susceptible organisms that each infected organism infects. ‘Infects’ carries the same meaning as ‘exposes’ in epidemic simulations such as SEIR simulation. ReproductionNumber reproduction number 1 Mathias Brochhausen Key motivating use case was Synthia synthetic population data. nursery school student population The fraction given to express the probability that an organism will become infected, but stay asymptomatic. The fraction of infectious individuals who do not develop symptoms during the course of their infections. asymptomatic infection fraction obsolete asymptomatic infection fraction true An action specification giving the number of doses of vaccine to be made available over a specific time period. The counts of vaccine doses that become available in a specific population location during (at the start of would be unambiguous) each simulator time step. vaccine supply schedule An action specification giving the number of vaccinations possible in a population during a specific time interval. The counts of individuals that could be vaccinated in a population location per time step unit in the absence of any vaccine supply constraints. It represents the capacity of medical system to vaccinate individuals. vaccination administration capacity The infectious disease treatment efficacy of an antiviral drug. The degree to which a particular antiviral drug reduces the probability that a treated individual will have a particular preventable outcome. Preventable outcomes include but are not limited to infection, infectiousness, symptoms, and hospitalization. AntiviralTreatmentEfficacy MB: For DL reasons the easiest way to formalize the definition was to assume only organism that are either host or not immune undergo antiviral treatment. Is that adequate? I assume this'll create problems… antiviral treatment efficacy The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role. The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection. antiviral efficacy delay The fraction expressing the probability that an organism will be consented to receive antiviral treatment when eligible. The fraction of individuals in a simulated population that will accept antiviral treatment if offered. antiviral cm compliance MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for an antiviral treatment against the members that are eligible and consented the antiviral treatment. There is a class "eligibility rule" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly. MW: Since the estimates that modelers use are from real populations, I have two questions: 1. Should we distinguish between real and simulated population? 2. If so, do we want to represent a ‘measured’ antiviral compliance number that is a property of a real population and distinguish it from this number that we are using to study what might happen in a simulated population? MB: This issue will need to be taken care of in the axiomatization of simulated population antiviral compliance An action specification giving the number of doses of an antiviral to be made available during a specific time interval. Counts of antiviral doses that become available in a specific location per time step unit. antiviral supply schedule An action specification that tells the total number of antiviral doses available to be administered to a population during a specific time interval. Counts of antiviral doses that can be administered in a specific location per time step unit. antiviral administration schedule A simulated organism that is assumed “eligible, willing and able” to participate with a particular control measure. A simulated organism in a simulated population that is “eligible, willing and able” to participate with a particular simulated control measure. MB: APOLLO_SV_00000053 and APOLLO_SV_00000058 have not been given a class restriction, since they are not expressible in BFO right now, due to their referring to "will". Both classes have been made disjoint in the OWL file, though. This class will need more ontological reasoning, since the "willing" part of the definition is not representable in BFO to date. simulation of organism awaiting control measure An identifier that refers to a specific simulator. Mathias Brochhausen The combination of simulator developer, simulator name, and simulator version, for example “www.psc.edu/FRED/2.0” The combination is intended to uniquely identify the simulation algorithm that produced output X, given input Y to support scientific audit, error analysis, and reproducibility of results. MB: I am not 100% happy with the elucidation. Can't we just say that this is the full identifier identifying the simulator with both its name and its version number? complete simulator identifier A simulating of a disease epidemic or pandemic. Mathias Brochhausen the process of simulating a disease epidemic or pandemic. This term is not currently used in Apollo-WS. epidemic simulation epidemic simulating Mathias Brochhausen Motivating use case is to cover Synthia data, and possibly configuration/output of the MRSA simulator in the MIDAS community (CA-MRSA Repast). hospital patient population census A simulated organism that is assumed “ineligible, unwilling or unable” to participate with a particular control measure. A simulated organism in a simulated population that is “ineligible, unwilling or unable” to participate with a particular simulated control measure. MB: APOLLO_SV_00000053 and APOLLO_SV_00000058 have not been given a class restriction, since they are not expressible in BFO right now, due to their referring to "will". Both classes have been made disjoint in the OWL file, though. This class will need more ontological reasoning, since the "unwilling" part of the definition is not representable in BFO to date. simulation of organism not awaiting control measure A simulated organism that participates in a particular control measure that has not yet been effective. This concept represents a simulated organism that has received a control measure such as vaccination in which a period of time must elapse before the benefit of the control measure accrues. A simulated organism is ‘awaiting efficacy’ if ‘efficacy delay’ (e.g. the concept ‘antiviral efficacy delay’ for the particular simulated control measure is greater than the elapsed time between application of the control measure and the current simulated time. simulation of organism awaiting effect of control measure The simulation of an antiviral control measure. A type of control measure based on administration of chemotherapeutic agents to an infected or high-risk organism that kill or inhibit replication of viruses within a simulated organism. antiviral control measure MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI). AND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess. Maybe we need to discuss this. simulation of antiviral control measure A simulation of a vaccination control measure. A type of control measure that uses vaccination to create immunity in simulated organisms to specific pathogens. simulation of vaccination control measure simulation of vaccination control measure 1 Key motivating use case was Synthia synthetic population data. primary school student population A simulation of an organism in a simulated population that has participated in an epidemic control measure. A simulated organism in a simulated population has participated in a particular simulated control measure. (e.g. an organism received antiviral treatment) simulation of control measure participant A time sampled measurement data set, where the position in the sequence of each data item corresponds to a specific time_step of the simulation. A sequence of data points, where the position in the sequence of each data point corresponds to a specific time_step of the simulation. MB: The ontological status of simulations (Thoughts) One property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating. While in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations. simulation time series A numeral that indexes a specific simulation. The run id indexes a run of a specific simulator version on a specific simulated population, disease(s), and optionally control measures. The simulator is responsible for generating a run id and ensuring its uniqueness. Class was originally created to correspond with an element from Apollo XSD v3.1.0. simulation identifier numeral A purely intentional entity that simulates a temporal interval of pre-specified length. A purely intentional entity that simulates a temporal interval of pre-specified length. simulation time step simulation of time step An action specification that specifies the length of the time steps interval assumed in a simulation. Mathias Brochhausen An action specification that specifies the length of the time steps interval assumed in a simulation. simulation time step value simulation time step unit simulation run length The time step value and unit are specified using a scalar value specification. simulation time step action specification A numeral that indexes a specific time step of a simulation. The time step number of a simulation. simulatorTime time step identifying numeral A purely intentional entity that simulates an entity and its properties. A purely intentional entity that simulates an entity and its properties. simulation simulation The simulation of geographical location in which a population is assumed to be located. An identifier referring to geographical location of a simulated population. Our intent is for the location identifiers to be INCITS codes. simulated population location obsolete simulation of population location true A simulation of a susceptible organism in a simulated population. A simulated organism in a simulated population that is capable of acquiring a particular simulated disease. simulation of susceptible organism A simulation of a symptomatic infectious agent host. A simulated organism in a simulated population that has at least one symptom caused by a particular simulated disease. simulation of symptomatic organism A simulation of an asymptomatic infectious agent host. A simulated organism in a simulated population that has no symptoms caused by a particular simulated disease. simulation of asymptomatic organism An objective specification that is realized by processes that are able or likely to stop the spread of a disease in a population. an objective of achieving satisfactory control of epidemic spread through a population typically, the process endpoint is achievement of R0 < 1 infectious disease control objective specification the mean or expectation of a distribution μ μ true standard deviation sigma σ true A continuous probability distribution whose characteristics and shape are determined by two parameters, alpha and beta. beta distribution beta distribution a continuous probability distribution over variable X whose parameters denoted μ and σ are, respectively, the mean and standard deviation of the variable’s natural logarithm deprecated log normal distribution true A continous probability distribution whose parameters a and b, denote its minimum and maximum values UniformDistribution uniform distribution a continuous probability distribution with lower limit a, upper limit b and mode c, where a < b and a <= c <= b. triangular distribution triangular distribution a discrete probability distribution BayesianNetwork Bayesian network a discrete probability distribution that conditions on time temporal Bayesian network temporal Bayesian network An action specification comprising the number of doses and their timing for administering a substance to an individual organism to prevent the negative effects of a specific infectious agent to that organism. A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism. control strategy dose schedule 1 age structure data set A data set consisting of measurements of age organized in age brackets. A data set consisting of measurements of age organized in age brackets. age data in age brackets data set A plan specification whose objective specification is an infectious disease control objective specification. A plan with the goal of preventing or mitigating the effects of infections in a population due to one or more pathogens. InfectiousDiseaseControlMeasure The essential goal of an infectious disease control strategy is to protect the susceptible organisms in a population. infectious disease control strategy The count of individuals in a susceptible population (empirical or virtual). The count of individuals in a susceptible population (empirical or virtual). count of susceptible population The count of individuals in an exposed population (empirical or virtual). The count of individuals in an exposed population (empirical or virtual). count of contacted population A measurement datum that is about a vaccination efficacy and is the specified output of a vaccination efficacy study. A vaccination efficacy that results from a vaccination efficacy study. VaccinationEfficacyMeasured 1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’ 2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer. measured vaccination efficacy a study design execution that has as its specified output one or more measured vaccination efficacy data items an experiment that measures vaccination efficacy from a sample of vaccinated and possibly unvaccinated individuals VaccinationEfficacyStudy vaccination efficacy study design execution an organism that has the property of being immune to a specific disease agent immune obsolete immune true a type of interval estimate of a population parameter used to indicate the reliability of an estimate. How frequently the observed interval contains the parameter is determined by the confidence level or confidence coefficient, in this type the confidence level is 95% 95% confidence interval 95% confidence interval a type of interval estimate of a population parameter that has the property that the true value of the estimated populatin parameter has a (specified) particular probability of being in the confidence interval given the data on which the estimate is derived. Baysesian credible interval Bayesian credible interval Two or more distinct populations that are part of the same biotic ecosystem. Two or more distinct populations that are part of the same biotic ecosystem. community William R. Hogan community a probability distribution over a discrete random variable discrete probability distribution deprecated discrete probability distribution true The increments of measurement for a measurable thing obsolete unit of measure true The sum of all biotic and abiotic entities in a geographical region. The sum of all biotic and abiotic entities in a geographical region. Ecosystem William R. Hogan ecosystem The count of individuals in a contagious population (empirical or virtual). The count of individuals in a contagious population (empirical or virtual). count of contagious population The count of individuals in a resistant population (empirical or virtual). The count of individuals in a resistant population (empirical or virtual). count of resistant population The abiotic ecosystem is the sum total of all continuants in a geographical region that are not organisms, parts of organisms, or dependent continuants that inhere in organisms. The abiotic ecosystem is the sum total of all continuants in a geographical region that are not organisms, parts of organisms, or dependent continuants that inhere in organisms. AbioticEcosystem William R. Hogan abiotic ecosystem An action specification that is part of a simulation software and specifies the time step numeral identifying the time step after which a simulation of a control strategy starts. The number of time steps after which a control strategy starts in a simulator. FixedStartTime fixed control strategy start time specification A rule that is part of an infectious disease control strategy specification and specifies at which fraction of a population a control strategy is to be discontinued. A fraction of a population that is targeted for treatment at which the control strategy is discontinued. The concept derives from the epidemiological notion of ‘herd immunity,’ which is a level of immunity in a population at which there are not enough susceptible individuals for a contagious disease to maintain the chain reaction. Technically, it is when the effective reproduction rate <= 1, which means that infectious individuals at most infect one person during the course of their illness. controlStrategyReactiveEndpointFraction control strategy reactive endpoint fraction The biotic ecosystem is the sum total of all organism populations in a particular geographical region. The biotic ecosystem is the sum total of all organism populations in a particular geographical region. BioticEcosystem William R. Hogan biotic ecosystem An identifier that refers to the legal person that creates and maintains software. An identifier that refers to the legal person that creates and maintains software. softwareDeveloper software developer identifier 1 An identifier that refers to a specific piece of software. An identifier that refers to a specific piece of software. SoftwareIdentification complete software identifier a fiat object part that is in gaseous phase and that is the outer layer of an object in space and is held to the object by gravitational force a fiat object part that is in gaseous phase and that is the outer layer of an object in space and is held to the object by gravitational force William R. Hogan atmosphere of Earth, Earth's moon, Saturn, Titan, etc. outer, gaseous layers of exoplanets are called extraterrestrial atmosphere. atmosphere An identifier that, as part of a complete software identifier, refers to one specific version of the software. An identifier that, as part of a complete software identifier, refers to one specific version of the software. softwareVersion software version identifier An identifier that refers to all version of a specific software. An identifier that refers to all version of a specific software. softwareName software identifier atmosphere of geographical region An educational institution is an place organization which provides the necessary system for people of different ages gain an education. It includes (among others) preschools, childcare, elementary schools, and universities. http://en.wikipedia.org/wiki/Types_of_educational_institutions (amended) An educational institution is an place organization which provides the necessary system for people of different ages gain an education. It includes (among others) preschools, childcare, elementary schools, and universities. obsolete educational institution true An information content entity about educational institutions that is part of the action sepcification of a school closure control measure. The specification of which facilities to target in a school closure control measure. school closure target facilities A reproduction of a pathogen organism of a particular biological taxon in a tissue of a host organism from another taxon. William R. Hogan infection process process of infection A process of reproduction of a particular pathogen species inside some tissue of a particular host species. M. Brochhausen infection is reproduction of a pathogen inside some tissue of a host. By associating infection with the classes latent period and infectious period, which are associated with specific pathogen species and host species, Apollo-SV defines infection further as reproduction of a particular pathogen taxon inside some tissue of a particular host taxon. infection The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources Mathias Brochhausen A process where a susceptible organism from a particular species becomes infected by a particular pathogen. The infection is acquired from an infected organism of a particular species or from a contaminated thing. Note that the susceptible and infectious organisms can be of different species. InfectionAcquisition Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use. The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things. The likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient. An infection is acquired from an infectious organism or a contaminated thing. Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing infection acquisition An identifier that refers to a type of vaccine, i.e., one of a class of manufactured vaccines that public health would consider interchangable. A unique identifier for a vaccine. vaccineOntologyId vaccine identifier Mathias Brochhausen latent period a unique identifier that refers to a protocol for vaccinating one person A unique identifier for a vaccination protocol (the process of vaccinating one person) vaccination identifier the number of doses of vaccine that are recommended to achieve immunity vaccination course an interbreeding population species species a unique identifier that refers to an antiviral drug product A unique identifier for an antiviral drug antiviralId antiviral identifier A place closure control strategy whose action specification is realized in a school closure process. A control measure in which schools are closed in an attempt to reduce transmission of disease. SchoolClosureControlStrategy school closure control strategy The number of time steps that a school closure control measure prescribes that schools will remain closed. school closure duration school closure duration The time steps that a school will be in session. school calendar true Faciilities that are the target of a control strategy control strategy target facilities control strategy target facilities A simulated population that is the target of a control strategy and its priority under triage conditions ControlMeasureTargetPopulationsAndPrioritization control strategy target populations and prioritization Fraction of organisms in a target population that a control strategy program seeks to enroll or prioritize a specification of a population that a control strategy applies to. It is intended to apply to a real population, so I don’t know whether you would consider it a simulated thing. I don’t. control strategy target population fraction an epidemic control measure plan specification that has a conditional specification as part a control measure (program) that is initiated or modified by an epidemic-related event (or if you prefer, an event occurring within/during the simulation) Reactive control measure obsolete Reactive control measure true An event in the ecosystem that triggers the starting or stopping of a control strategy. reactiveControlMeasureTest reactive control strategy test A data item that specifies the fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy. A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy. The event could be infection acquisition, vaccination, antiviral treatment, etc. reactiveControlMeasureThreshold reactive control strategy threshold 1 Key motivating use case was Synthia synthetic population data. secondary school student population A measurement datum of the time interval from the decision to implement an infectious disease control strategy to the start of the control strategy expressed in number of time intervals. A period from the initiation of a control strategy until its disease-controlling actions actually begin. For example, once a vaccination control strategy starts, individual vaccinations may not occur right away: it might take some time until workers and vaccines are deployed and ready to begin. controlMeasureResponseDelay control strategy response delay Number of time steps it takes medical personnel to ascertain a symptomatic individual from onset of symptoms per Mike Wagner, this is input ascertainment delay Fraction of all symptomatic individuals who will be ascertained fractionInState fraction of organisms (usually infected) that a surveillance system detects out of the total population ascertainment fraction An individual treatment control strategy that has as part an action specification that is realized in a vaccination process. An individual treatment control strategy that administers one or more vaccines to individuals in a population with the goal of inducing resistance to infection with a particular pathogen in those individuals. vaccination control strategy the number of distinct antigenic strains in a vaccine product valence vaccine valence An action specification that tells how many doses of antiviral drug should be given to each individual that participates in the antiviral control measure. The quantity of antiviral drug used to treat one individual antiviral course A measurement datum about the fraction of individuals in a population that elect to participate in a control strategy when offered. A fraction of eligible individuals in a population who receive an intervention or participate in a control strategy. compliance the class restriction can be made more precise AH the fraction of some population that is targeted for a control strategy that accepts it. It can obviously also be interpreted as a probability that the average individual in the targeted population accepts/complies with the control strategy. It is not simulated control strategy compliance Mathias Brochhausen infectious period Mathias Brochhausen protect against effect of pathogen A treatment that consists of the administration of antigenic material to stimulate an individual's immune system to develop adaptive immunity to a pathogen. Mathias Brochhausen http://en.wikipedia.org/wiki/Vaccination A treatment of an individual with antigenic material from a pathogen that has the goal of inducing resistance of the individual to infection with the pathogen. Vaccination vaccination Mathias Brochhausen replaced with VO 'vaccine function' vaccine disposition true Mathias Brochhausen disposition to become contaminated with a pathogen The dispostion of an organism of a particular biological taxon A that is realized by inhibiting the establishment of an infection by an organism of another particular biological taxon that bears an infectious disposition towards members of A Mathias Brochhausen William R. Hogan Key issue with equivalent class axiom is how to say that this scattered molecular aggregate is both 1) not originally part of the organism and/or 2) is temporary. I suppose baby could be born with drug acquired from its mother's system. Somehow, it's not innate and it's temporary, ie, the body will eventually clear it. The dispostion of an organism of a particular biological taxon A that is realized by inhibiting the establishment of an infection by an organism of another particular biological taxon that bears an infectious disposition towards members of A resistance to infection Transmission parameter (sometime known as Ptrans). This value is multiplied by the inter-personal contact probability to determine the transmission probability between infected and susceptible persons. it is the same thing as transmission coefficient beta true Transmission parameter inter-personal contact probability inter-personal contact probability random number seed random number seed true A number between 0 and 1 indicating the degree of susceptibility of an organism susceptibility measurement datum a fraction of the target population, that once vaccinated, results in stopping further vaccination in the population vaccination reactive end point fraction Resistance to infection that is conferred by immune system/immune mechansisms. Mathias Brochhausen Resistance to infection that is conferred by immune system/immune mechansisms. immune resistance to infection A planned process involving counting numbers of a organism population, possibly including counting sub-populations fulfilling specific criteria, and that realizes some concretization of a census objective specification. Mathias Brochhausen A planned process involving counting numbers of a organism population, possibly including counting sub-populations fulfilling specific criteria. population survey A census that is the outcome of a population survey. A census that is the outcome of a population survey. population census A population of host organisms undergoing infection and that are not infectious. A population of host organisms undergoing infection and that are not infectious. exposed population exposed population A population survey that counts the number of individuals in the population who are infected with a particular pathogen. Mathias Brochhausen A population survey that counts the number of individuals in the population who are infected with a particular pathogen. PopulationInfectionSurvey Comment from Mike (to do!): I checked because an infection and immunity census would involve two different census methods. One would be some kind of disease surveillance that counts infections. The other is some kind of immunity census process based on seroprevalence studies or vaccination registries. Equivalent class was: 'population survey' and (has_part some (counting and (has_specified_output some (count and ('is about' some 'exposed population'))) and (has_specified_output some (count and ('is about' some 'infectious population'))) and (has_specified_output some (count and ('is about' some 'susceptible population'))) and (has_specified_output some (count and ('is about' some 'immune population'))))) population infection survey A population of host organisms undergoing infection that are contagious. A population of host organisms undergoing infection that are contagious. contagious population A census that is the result of a population infection survey and a population immunity survey. Mathias Brochhausen PII Census A census of the infection status (e.g., susceptible, infected, infectious, and immune/resistant) of organisms in a population, with respect to a particular pathogen. PopulationInfectionAndImmunityCensus population infection and immunity census population demographic survey A census that is the specific outcome of a population demographic survey. Mathias Brochhausen A census that is the specific outcome of a population demographic survey. population demographic census Mathias Brochhausen obsolete contamination true An ecosystem in which a population of hosts is undergoing at least one infection. Mathias Brochhausen An ecosystem in which a population of hosts is undergoing at least one infection. MIDAS scenario true An information content entity that is about a MIDAS scenario and contains population disease census data. Mathias Brochhausen An information content entity that is about a MIDAS scenario and contains population disease census data. need to change the text definition. need to change label to be more consistent with current Apollo terminology (possibly 'infectious disease scenario'. MIDAS scenario representation A population of organisms that have been infected, but are no longer able to transmit the disease and to acquire the infection again. Mathias Brochhausen recovered population synthetic ecosystem constructing A planned process that has one or more synthetic ecosystem datasets as output. Mathias Brochhausen Matthew Diller William R. Hogan creating a synthetic ecosystem dataset synthetic ecosystem generating A planned process that has one or more synthetic ecosystem datasets as output. agent-level ecosystem data generation A census that is the specified output of a agent-level ecosystem data generation that had census data as an input. Mathias Brochhausen A census that is the specified output of a agent-level ecosystem data generation that had census data as an input. agent-level ecosystem census An independent continuant that is the localization of a pathogen, but is not undergoing an infection. Mathias Brochhausen An independent continuant that is the localization of a pathogen, but is not undergoing an infection. ContaminatedThing A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection. contaminated thing A biological process whereby an entity that is not in contact with a pathogen of a particular biological taxon begins to undergo contamination with that pathogen. Mathias Brochhausen William R. Hogan A biological process whereby an entity that is not in contact with a pathogen of a particular biological taxon begins to undergo contamination with that pathogen. ContaminationAcquisition contamination acquisition Motivating use case is Synthia synthetic population data. nursery school student population census Motivating use case is Synthia synthetic population data. primary school student population census Motivating use case is Synthia synthetic population data. secondary school student population census A treatment with an antiviral drug. A treatment of a particular host with a particular antiviral drug with activity against a particular viral pathogen. AntiviralTreatment antiviral treatment The ability to participate in infection acquisition as a host. Mathias Brochhausen The ability to participate in infection acquisition as a host. susceptibility A data set of a specific entity in a specified region at a specified time. Mathias Brochhausen A data set of a specific entity in a specified region at a specified time. CensusData census An algorithm that models the progress of a transmissible disease in a population. An algorithm that models the progress of a transmissible disease in a population. disease transmission model disease transmission model An organization created with the purpose of providing education to those of its members that are bearer of student role. Mathias Brochhausen An organization created with the purpose of providing education to those of its members that are bearer of student role. obsolete school organization true Mathias Brochhausen Motivating use case is Synthia synthetic population data. school student population census 1 The collection of students administrated by exaclty one school organization. Mathias Brochhausen The collection of students administrated by exaclty one school organization. Key motivating use case was Synthia synthetic population data. school student population An information content entity that contains everything a simulator needs to run, including the representation of a scenario. An information content entity that contains everything a simulator needs to run, including the representation of a scenario. simulatorConfiguration simulator configuration A human social role that is realized by attending a school to receive formal education. Mathias Brochhausen A human social role that is realized by attending a school to receive formal education. obsolete student role true An anti-infective individual treatment control strategy that has as part an action specification that is realized in antiviral treatment. Mathias Brochhausen An anti-infective individual treatment control strategy that uses anti-viral medications to treat infected hosts in an attempt to limit their infectiousness and/or infectious period. antiviral control strategy contagiousness An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps). An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps). SimulatorTimeSpecification simulator time specification A dataset that represents at least one pathogen population (of a particular biological taxon) in one host population (of a particular biological taxon) in an ecosystem in a particular location at a particular point in time. William R. Hogan Data about an infection in an ecosystem at a specific location and point in time. InfectiousDiseaseScenario An infectious disease scenario contains counts of infections of a particular pathogen in a particular host in a particular ecosystem at a particular point in time, minimally. Agent-based ecosystems represent each host individually. The infectious disease scenario typically also includes a lot of additional data about the ecosystem, including data about things like transmission probabililites, control measures, the immunity or other resistance status of host individuals, and so on. infectious disease scenario An identifier that denotes a real date corresponding to simulator time zero. A reference to the date that corresponds to simulator time zero. scenarioDate scenario date biological contamination The process of existence without reproduction of a pathogen of a particular biological taxon in or on some material entity or the process of reproduction of a pathogen in or on a material entity that is not an organism. William R. Hogan The process of existence without reproduction of a pathogen of a particular biological taxon in or on some material entity or the process of reproduction of a pathogen in or on a material entity that is not an organism. Contamination the preferred term is biological contamination to distinguish from things like radiological contamination, contamination of the Gulf of Mexico with oil, the contamination of air with pollution, etc. contamination A census about a particular medical treatment of a population. A census of a population that determines for a particular treatment whether each organism in the population has undergone that treatment. PopulationTreatmentCensus population treatment census A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero. A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero. Class was originally created to correspond with a complex type from Apollo XSD v3.1.0. This census should exclude infection, immunity, treatment, or contamination. population and environment census A census that is the outcome of assessing control-strategy-related facilities and supply chains. A census that is the outcome of assessing control-strategy-related facilities and supply chains. control strategy inventory census A host who is able to transmit some infection to another organism. An infected organism of a particular species who is able to transmit the infection to a susceptible organism of a particular species. Note that the infected and susceptible organisms may be of different species. infectious contagious organism An information content entity that represents the rate that an infection moves from infected individuals to susceptible individuals in a population. An information content entity that represents the rate that an infection moves from infected individuals to susceptible individuals in a population. beta transmission coefficient A data item specifying a measured vaccination efficacy. A data item specifying a measured vaccination efficacy. obsolete vaccination efficacy measured true A data item inferring a vaccination efficacy based on epidemiological data. A data item inferring a vaccination efficacy based on epidemiological data. VaccinationEfficacyInferred vaccination efficacy inferred vaccination control strategy, antiviral control strategy An infectious disease control strategy that immediately targets individuals. Mathias Brochhausen An infectious disease control strategy that immediately targets individuals. IndividualTreatmentControlMeasure individual treatment control strategy An organism population that is the target for a disease control strategy. An organism population that is the target for a disease control strategy. TargetPopulation target population ring vaccination individual treatment control strategy An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved. agent level population and environment census At present, this class corresponds with an XSD type that contains authentication plus information needed to generate a Synthia synthetic population dataset including (1) geographical location and (2) a list of household characteristics. agent model ecosystem census description true The Apollo XSD allows us to specify counts of certain subpopulations and abiotic ecosystem elements for a compartmental model (vs. specifying each individual in the population as in agent model population and environment census). compartment model population and environment census true PopulationStrataDefinition population strata definition A census about contaminated things of a given type in an area of interest. A census about contaminated things of a given type in an area of interest. ContaminatedThingCensus contaminated thing census ApolloIndexableItem A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved. indexable Apollo item A taxonomy identifier curated by the NCBI Taxonomy that designates a biological taxon. An identifier curated by the National Center for Biotechnology Information (NCBI) that designates a particular biological taxon (e.g., Homo sapiens). NcbiTaxonId NCBI taxon identifier A processual entity that is either the outcome of a disease course or a part of a disease course and has etiological relevance. William R. Hogan An event that happens during the course of a disease and that results from pathological processes that happened earlier in the disease. diseaseOutcome The infectious disease type in the XSD has a disease outcome element, which specifies whether someone became symptomatic, was hospitalized, etc. All of these outcomes require some process to occur. For sequalae of disease, it is that the realization of the disease is an etiological process that creates some other disorder. For example, fever is often occurs because of high levels of certain interleukins (which is a disorder). So I am comfortable with disease outcome as a process. It is also consistent with the probabilitistic information that will go with it, as a future probability is almost always (if not always) the probability of some event occurring (e.g., coin turning up heads, raining, developing a disease), disease outcome An organism that is the bearer of a susceptibility disposition. William R. Hogan An organism of a particular species that can undergo infection with a particular pathogen. susceptible susceptible organism An organism that is the bearer of an immune resistance disposition. William R. Hogan An organism of a particular species that has developed immune resistance to infection with a pathogen of a particular species. immune immune organism an organism that is the bearer of resistance to infection William R. Hogan An organism of a particular species that is unable to undergo infection with a particular pathogen. resistant resistant organism An information content entity that specifies the start time of the implementation of a infectious disease control strategy. A specification of when an infectious disease control strategy starts. controlMeasureStartTime control strategy start time information organism in latent period of infection An infectious agent host who is NOT able to transmit the infection to another organism of the same species. William R. Hogan An infected organism of a particular species that is not yet able to transmit the infection to a susceptible organism of a particular species. Note that the infected and sucseptible organisms may be of different species. infected infected organism A simulator configuration that start an Apollo simulator. Mathias Brochhausen A simulator configuration that start an Apollo simulator. RunSimulationMessage apollo simulator configuration The probability of the occurence of an infection acquisition from one infected organism to another when in contact. The probability of the occurence of an infection acquisition from one infected organism to another when in contact. TransmissionProbability transmission probability A plan specification that specifies the capacity to administer a particular treatment over a specific temporal interval in a specified geographical region. A specification of how many doses (of material) of an individual treatment can be administered per unit time in a particular geographical location. capacitySchedule treatment administration capacity schedule A schedule that specifies the availability of a particular drug over a specific temporal interval in a specified geographical region. Mathias Brochhausen A specification of how many doses (of material such as drug or vaccine) of a treatment become available per unit time in a particular geographical location. supplySchedulePerDay treatment supply schedule An information content entity that specifies the vaccination efficacy that is part of a simulator configuration. Mathias Brochhausen An information content entity that specifies the vaccination efficacy that is part of a simulator configuration. VaccinationEfficacyForSimulatorConfiguration vaccination efficacy for simulator configuration An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. http://en.wikipedia.org/wiki/Probability_distribution An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. ProbabilityDistribution probability distribution a probability distribution over a discrete random variable a probability distribution over a discrete random variable discrete probability distribution A data item that specifies the epidemiologically-relevant state of a host organism at a specific time with respect to infection with a particular pathogen. Mathias Brochhausen A data item that specifies the epidemiologically-relevant state of a host organism at a specific time with respect to infection with a particular pathogen. infectionState infection state data item An objective specification that specifies the disease outcome a vaccination seeks to prevent. Mathias Brochhausen An objective specification that specifies the disease outcome a vaccination seeks to prevent. vaccinationPreventableOutcome vaccination preventable outcome An information content entity that designates a biological taxon and optionally a clade of pathogens. Mathias Brochhausen An identifier that represents the taxonomy of a pathogen by a required NCBI Taxonomy identifier AND an optional clade name. The clade name is a string in XSD version 2.0.1. ApolloPathogenCode Apollo pathogen code A material entity that is part of an abiotic ecosystem. Mathias Brochhausen A material entity that is part of an abiotic ecosystem. Class was originally created to correspond with an element from Apollo XSD v3.1.0. abiotic ecosystem element An immune population that acts as the members know they are immune (do not seek vaccination/antiviral treatment, etc.). Mathias Brochhausen An immune population that acts as the members know they are immune (do not seek vaccination/antiviral treatment, etc.). immune population acting like immune An immune population that acts as the members assume they are not immune (e.g. seek vaccination/antiviral treatment). Mathias Brochhausen An immune population that acts as the members assume they are not immune (e.g. seek vaccination/antiviral treatment). immune population acting like not immune The process of an organism stopping to experience any symptoms caused by a disease. Mathias Brochhausen The process of an organism stopping to experience any symptoms caused by a disease. asymptomatic becoming asymptomatic The process of an organism beginning to experience symptoms caused by a disease. Mathias Brochhausen The process of an organism beginning to experience symptoms caused by a disease. symptomatic becoming symptomatic The process of an organism beginning to experience severe symptoms caused by a disease. Mathias Brochhausen The process of an organism beginning to experience severe symptoms caused by a disease. severely symptomatic becoming severely symptomatic A process profile that specifies the degree to which a host is likely to pass on an infection to a susceptible organism. Mathias Brochhausen A process profile that specifies the degree to which a host is likely to pass on an infection to a susceptible organism. infectiousnessProfile This is probably a 'process profile' according to BFO2 infectiousness profile The disposition of one or more portions of material entity, when administered to a susceptible organism by a certain route and according to a certain schedule, to produce a structural change in an organism of a specific species, whereby this structural change serves as the physical basis of a protective resistance disposition. William R. Hogan The disposition of one or more portions of material entity, when administered to a susceptible organism by a certain route and according to a certain schedule, to produce a structural change in an organism of a specific species, whereby this structural change serves as the physical basis of a protective resistance disposition. TreatmentEfficacy need to generate class restriction. Something like: 'is realized by' some (processual_entity and (has_participant some ('Anatomical structure' and ('is physical basis of' some 'protective resistance')) we'd also like to say that the protective resistance disposition began to exist during the process. can't recall whether we should use process or processual_entity for future BFO compatibility. infectious disease treatment efficacy A travel-related infectious disease control strategy that has an action specification that is realized in restricting movement of organisms across international borders. William R. Hogan A travel-related infectious disease control strategy that has an action specification that is realized in restricting movement of organisms across international borders. BorderControlMeasure border control strategy an infectious disease control strategy that has an action specification that is realized in closing facilities where organisms congregate during times when the facilities normally would be open. William R. Hogan An infectious disease control strategy that attempts to prevent infection of susceptible host organisms in a population by preventing potentially infectious contacts (for a particular pathogen) among the organisms in the population. PlaceClosureControlMeasure place closure control strategy an infectious disease control strategy that has an action specification that is realized in isolating organsims who are infectious. William R. Hogan An infectious disease control strategy that isolates infected and/or infectious individuals in a population from most or all potentially infectious contacts with susceptible individuals. CaseQuarantineControlMeasure case isolation control strategy A travel-related infectious disease control strategy whose action specification is realized in restricting travel of organims from one ecosystem to another ecosystem William R. Hogan A travel-related infectious disease control strategy whose action specification is realized in restricting travel of organims from one geographical region to another TravelRestrictionControlMeasure travel restriction control strategy A taxonomy identifier that denotes a group of organisms or groups of organisms based on common ancestors. Mathias Brochhausen A reference to a group or groups of organisms that are based on common ancestry. cladeName Some regard a clade to be a single branch on the tree of life. [http://en.wikipedia.org/wiki/Clade] clade name A population of only infected members of one species. A population of only infected members of one species. infected population A population of organisms that are all susceptible. A population of organisms that are all susceptible. susceptible population A population of organisms that are all immune. A population of organisms that are all immune. immune population asymptomatic host An organism of a particular biological taxon that is the bearer of an infectious dispositions towards an organism of a different particular biological taxon. An organism, virus, or prion that can infect another organism. pathogen pathogen An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon. An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon. host host organism A disease that inheres in a host and, when realized, is realized as a disease course that is causally preceded by an infection. A disease that is caused by an infection. InfectiousDisease Infection is the etiological process, as defined by OGMS, for infectious disease. However, OGMS does not relate its etiological process class to its disorder class as of this writing. So it is not clear how to connect infectious disease to its infection etiological process. infectious disease A information content entity that specifies the date of a census. Mathias Brochhausen A information content entity that specifies the date of a census. referenceDate census reference date An information content entity specifying the upper and lower limit of a range of ages of continuants. Mathias Brochhausen An information content entity specifying the upper and lower limit of a range of ages of continuants. AgeRangeCategoryDefinition age range category A name of temporal region that specifies a time span on a specified time scale by giving a start time and a duration. Mathias Brochhausen An information content entity that specifies a time span on a specified time scale by giving a start time and a duration. TimeSpanCategoryDefinition name of temporal interval A measurement datum that quantifies a temporal region that is occupied by a processual entity. Mathias Brochhausen A measurement datum that quantifies a temporal region that is occupied by a processual entity. Duration duration a unique identifier that refers to a disease. Mathias Brochhausen A unique identifier that refers to a particular type of disease. This class is different from its superclass, in that the identifier is non-redundant with other identifiers in its context (such as a coding system or terminology or ontology). The superclass admits of natural langugage names of diseases, whereas this one typically does not. We still need to decide which coding schema to adopt.-MB disease unique identifier A probability distribution of two jointly distributed random variables X and Y, where Y is know to be a particular value. Mathias Brochhausen A probability distribution of two jointly distributed random variables X and Y, where Y is know to be a particular value. ConditionalProbabilityDistribution conditional probability distribution In the study of probability, given at least two random variables X, Y, ..., that are defined on a probability space, the joint probability distribution for X, Y, ... is a probability distribution that gives the probability that each of X, Y, ... falls in any particular range or discrete set of values specified for that variable. Mathias Brochhausen http://en.wikipedia.org/w/index.php?title=Joint_probability_distribution&oldid=599692661 In the study of probability, given at least two random variables X, Y, ..., that are defined on a probability space, the joint probability distribution for X, Y, ... is a probability distribution that gives the probability that each of X, Y, ... falls in any particular range or discrete set of values specified for that variable. joint probability distribution An unconditional probability distribution is the probability distribution of an uncertain variable, U, implicitly incorporating the uncertainty introduced by any other relevant variables. Mathematically, U’s unconditional probability distribution is written {U | E}, where E represents the background state of information under which the distribution is assessed. Mathias Brochhausen http://grahamjeffery.com/glossary/213-unconditional-probability-distribution An unconditional probability distribution is the probability distribution of an uncertain variable, U, implicitly incorporating the uncertainty introduced by any other relevant variables. Mathematically, U’s unconditional probability distribution is written {U | E}, where E represents the background state of information under which the distribution is assessed. UnconditionalProbabilityDistribution unconditional probability distribution Mathias Brochhausen ParametricProbabilityDistribution obsolete parametric probability distribution true Mathias Brochhausen http://purl.obolibrary.org/obo/STATO_0000321 NonparametricProbabilityDistribution nonparametric probability distribution true Mathias Brochhausen DiscreteParametricProbabilityDistribution discrete parametric probability distribution Mathias Brochhausen ContinuousParametricProbabilityDistribution continuous parametric probability distribution Mathias Brochhausen DiscreteNonparametricProbabilityDistribution discrete nonparametric probability distribution Mathias Brochhausen continuous nonparametric probability distribution A continuous parametric probability distribution that takes as its input a normally-distributed logarithmic function with mean μ and standard deviation σ. Mathias Brochhausen http://en.wikipedia.org/w/index.php?title=Log-normal_distribution&oldid=601643223 a log-normal (or lognormal) distribution is a continuous probability distribution of a random variable whose logarithm is normally distributed. LogNormalDistribution log normal distribution the gamma distribution is a two-parameter family of continuous probability distributions Mathias Brochhausen http://en.wikipedia.org/w/index.php?title=Gamma_distribution&oldid=602019254 the gamma distribution is a two-parameter family of continuous probability distributions GammaDistribution gamma distribution A continuous parametric probability distribution that gives the distribution of lifetimes of objects. It was originally proposed to quantify fatigue data, but it is also used in analysis of systems involving a "weakest link." Mathias Brochhausen A continuous parametric probability distribution that gives the distribution of lifetimes of objects. It was originally proposed to quantify fatigue data, but it is also used in analysis of systems involving a "weakest link." WeibullDistribution Weibull Distribution the continuous uniform distribution or rectangular distribution is a family of symmetric probability distributions such that for each member of the family, all intervals of the same length on the distribution's support are equally probable. Mathias Brochhausen http://en.wikipedia.org/w/index.php?title=Uniform_distribution_(continuous)&oldid=597643343 the continuous uniform distribution or rectangular distribution is a family of symmetric probability distributions such that for each member of the family, all intervals of the same length on the distribution's support are equally probable. ContinuousUniformDistribution continuous uniform distribution The duration between the appearance of symptoms of a disease and the start of a treatment. Mathias Brochhausen The duration between the appearance of symptoms of a disease and the start of a treatment. delayFromSymptomsToTreatment delay from symptoms to treatment An identifier that refers to a particular geographical region and that is constructed per guidelines of the Apollo project. A hierarchical identifier beginning with an ISO 2-letter nation code (e.g., US) and that represents one partition of an exclusive and exhaustive partitioning of that nation (including the trivial case of just representing the entire region of the nation). ApolloLocationCode William R. Hogan apollo location code An information content entity that specifies the time at which an infectious disease control strategy ends. An information content entity that specifies the time at which an infectious disease control strategy ends. controlMeasureStopTime William R. Hogan control strategy stop time information A rule that specifies the event that, when it occurs, is the trigger to either start or stop an infectious disease control strategy. A rule that says when to start or stop a control strategy. It can be either the passage of time, a disease surveillance result (exceeding the threshold of a certain fraction of the population that is infected), or a treatment surveillance result (reaching a certain fraction of the population that has received an antiviral or vaccination). TriggerDefinition William R. Hogan infectious disease control strategy trigger definition The probability of the occurence of a contamination acquisition from either an infected organism or another contaminated thing. The probability of the occurence of a contamination acquisition from either an infected organism or another contaminated thing. William R. Hogan contamination probability A measurement datum of the time interval from the decision to cease an infectious disease control strategy to the time the control strategy ends expressed in number of time intervals. A period from the conclusion of a control strategy until its disease-controlling activities actually end. For example, it may take time to communicate to workers to stop vaccinating and thus they keep vaccinating for some time after the control strategy is concluded. controlMeasureStandDownDelay William R. Hogan control strategy stand-down delay An infection acquisition whereby a susceptible host acquires an infection from a contaminated thing. William R. Hogan An infection acquisition from a contaminated thing. InfectionAcquisitionFromContaminatedAbioticThing infection acquisition from contaminated thing An infection acquisition whereby a susceptible host acquires an infection from an infectious host. William R. Hogan An infection acquisition from an individual who is infectious. The individual acquiring the infection can be of a different species than the one who is infectious. InfectionAcquisitionFromInfectedHost infection acquisition from infectious host A disposition of a disease surveillance infrastructure to detect the outbreak of one particular disease in the geographical region the infrastructure aims to cover. Mathias Brochhausen A capability associated with a location to detect individuals in a population with a particular type of disease. DiseaseSurveillanceCapability Specifies location, pathogen, host taxon, caseDefinition, sensitivity, specificity, and time delay of case detection disease surveillance capability The duration from the time an organism satisfies a case definition until a process or system detects the organism as satisfying that case definition Mathias Brochhausen The period from the time an organism satisfies the criteria of a case definition until a process or system detects the organism as satisfying those criteria. timeDelayToCaseDetection time delay to case detection An identifier that designates a scale according to which time is measured (e.g., Gregorian Calendar). William R. Hogan A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time. In epidemic simulation, it can be 'simulator time' where time zero is the starting point of an infectious disease scenario, or it can be 'control strategy time' where time zero is the time at which the control strategy is initiated. timeScale time scale name An infectious disease control trigger definition for a reactive control measure based on the outcome of disease surveillance. Mathias Brochhausen A control strategy trigger that occurs once a particular disease surveillance event occurs. For example, the trigger could occur once the incidence or prevalence of the infectious disease exceeds a fixed threshold. DiseaseSurveillanceTriggerDefinition disease surveillance trigger definition An infectious disease control trigger definition for a reactive control measure based on the outcome of disease surveillance. Mathias Brochhausen An infectious disease control trigger definition for a reactive control measure based on the outcome of disease surveillance. TreatmentSurveillanceTriggerDefinition treatment surveillance trigger definition An infectious disease control trigger definition that is based on the passage of a specified interval of time. A control strategy trigger that occurs once a constant duration of time has elapsed. TemporalTriggerDefinition temporal trigger definition the duration of time that has elapsed from the zero reference point to a later time on the time scale William R. Hogan A duration of time that has elapsed since the zero reference point of a time scale. timeSinceTimeScaleZero time since time scale zero SeasonalityFunctionParameters seasonal function parameter maximumSeasonalLatitude maximum seasonal latitude minimumSeasonalLatitude minimum seasonal latitude seasonalTemporalOffset seasonal temporal offset The sensitivity of a system that classifies organisms into the binary categories of individual who meets the criteria of a particular case definition and individual who does NOT meet the criteria of a particular type of disease X. The sensitivity of a process or system that detects organisms who satisfy a case definition. sensitivityOfCaseDetection sensitivity of case detection The probability that entry is denied as part of a border control strategy. Mathias Brochhausen The probability that entry is denied as part of a border control strategy. probabilityEntryDenied probability of entry into a country is denied The probability that exit is denied as part of a border control strategy. Mathias Brochhausen The probability that exit is denied as part of a border control strategy. probabilityExitDenied probability of exit from a country is denied A duration that measures the temporal interval occupied by a treatment course. Mathias Brochhausen A period from the start to the end of a treatment course. durationOfTreatmentCourse duration of treatment course The count of the number of doses that are part of a treatment course. Mathias Brochhausen The number of doses (of material such as antiviral drug or vaccine) that constitutes a particular course of treatment numDosesInTreatmentCourse number of doses in a treatment course A specification of the target populations of a control strategy and the priority of each population in the strategy. targetPopulationsAndPrioritizations target populations and prioritizations information An epidemic simulator action specification that specifies the factor by which to multiply the transmission coefficient for contacts that occur in a school. Matthew Diller William R. Hogan A factor by which to multiply the transmission coefficient for contacts that occur in in a school. schoolTransmissionMultiplier school transmission multiplier An epidemic simulator action specification that specifies the factor by which to multiply the transmission coefficient for contacts that occur in a household. Matthew Diller William R. Hogan A factor by which to multiply the transmission coefficient for contacts that occur in a household. householdTransmissionMultiplier household transmission multiplier An epidemic simulator action specification that specifies the factor by which to multiply the transmission coefficient for contacts that occur in a workplace. Matthew Diller William R. Hogan A factor by which to multiply the transmission coefficient for contacts that occur in a workplace. workplaceTransmissionMultiplier workplace transmission multiplier A place-closure control strategy that decides on a case-by-case basis whether to close places of a certain type, as opposed to blanket policy that closes all places of a certain type at the same time. A place-closure control strategy that decides on a case-by-case basis whether to close places of a certain type, as opposed to blanket policy that closes all places of a certain type at the same time. closeIndividualPlacesIndependently close individual places independently strategy The duration from the closure of a place until the time when it is reopened. William R. Hogan closurePeriod place closure period communityTransmissionMultiplier community transmission multiplier maximumTravelDistanceInKm maximum travel distance in km information An objective specification that specifies the disease outcome that a treatment seeks to prevent. William Hogan An objective specification that specifies the disease outcome that a treatment seeks to prevent. TreatmentPreventableOutcome treatment preventable outcome The duration from the time an individual receives a treatment until the time a system designed to detect that the treatment occurred detects it in a population William R. Hogan The duration from treatment until a treatment surveillance system detects it in a population timeDelayOfTreatmentDetection time delay of treatment detection The unit of measure for the supply schedule of an individual treatment. William R. Hogan The unit of measure for the supply schedule of an individual treatment. For example, 'daily dose'. supplyScheduleUnits individual treatment strategy supply schedule unit of measure William R. Hogan The unit of measure for the administration capacity of an individual treatment. For example, 'daily dose'. administrationCapacityUnits individual treatment strategy administration capacity unit of measure William R. Hogan A disease transmission model that explicitly represents each individual in the population and simulates the acquisition of disease by individuals who do not already have it at simulator time zero. agent-based disease transmission model A unit of measure for a threshold in a reactive infectious disease control strategy. William R. Hogan A unit of measure for a threshold in a reactive infectious disease control strategy. unitOfMeasureForThreshold reactive control strategy threshold unit of measure An information content entity that specifies the criteria that an organism must meet to be considered to be in some abnormal state. William R. Hogan A specification of the criteria an organism must meet to be considered to be in some abnormal state. The abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on. CaseDefinition case definition William R. Hogan A period during which an infectious host organism is isolated from contact with other organisms in the ecosystem as part of a quarantine control strategy. obsolete quarantine period true A process whose beginning is demarcated by accelerating infection acquisition by one or more host species of a particular pathogen in a particular location and whose end is demarcated by the time when the rate of infection acquisition becomes constant. William R. Hogan epidemic of infection A process whose beginning is demarcated by accelerating infection acquisition by one or more host species of a particular pathogen in a particular location and whose end is demarcated by the time when the rate of of infection acquisition becomes constant. The constant rate may be zero. The period of an epidemic may be defined using statistical criteria based on incidence rates or causal models based on their fit to incidence data. Epidemic An example of multiple host species is foot and mouth disease (such as the 2001 epidemic in the UK, see: http://www.sciencemag.org/content/292/5519/1155.long) and swine flu. The foot and mouth disease epidemic affected sheep, pigs, and cattle. epidemic An immune organism that acts as if it is immune (i.e., it does not seek vaccination or avoid contact with infectious organisms). William R. Hogan An organism of a particular species who is immune to infection with a pathogen of a particular species, and that acts as if it is immune (that is, it does not seek vaccination, avoid contact with infectious organisms, etc.) immuneAndActsLikeImmune immune organism that acts like it is immune An immune organism that acts as if it is NOT immune (i.e., it seeks vaccination and/or avoids contact with infectious organisms). William R. Hogan An organism of a particular species who is immune to infection with a pathogen of a particular species, and that acts as if it is NOT immune (that is, it does seeks vaccination, avoids contact with infectious organisms, etc.) immuneButActsLikeNotImmune immune organism that acts like it is not immune An immune resistance to infection that is causally preceded by an infection and an immune response to that infection with the production of antibodies to antigens from the pathogen population participating in the infection. William R. Hogan An immune resistance to infection that is causally preceded by an infection and an immune response to that infection with the production of antibodies to antigens from the pathogen population participating in the infection. naturally-acquired active immune resistance An organism that is the bearer of a naturally-acquired, active immune resistance to infection. William R. Hogan An organism that has recovered from infection with a particular pathogen, is no longer infectious to other organisms of any species, and is not able to be infected again with that pathogen. recovered recovered organism A disease transmission model that represents populations of susceptible and infected individuals (but not these individuals directly themselves) and simulates movement of individuals from one such population (a.k.a. compartment) to another. compartmental disease transmission model An individual treatment control strategy that has as part an action specification that is realized in anti-infective treatment. William R. Hogan An anti-infective individual treatment control strategy that uses anti-infective medications to treat infected hosts in an attempt to limit their infectiousness and/or infectious period. DrugTreatmentControlStrategy anti-infective control strategy anti-infective individual treatment control strategy An anti-infective individual treatment control strategy that has as part an action specification that is realized in antibacterial treatment. William R. Hogan An anti-infective individual treatment control strategy that uses anti-bacterial medications to treat infected hosts in an attempt to limit their infectiousness and/or infectious period. anti-bacterial control strategy infection in an ecosystem A process comprised of numerous infections and infection acquisitions with a particular pathogen in one or more populations of hosts. William R. Hogan A process of ongoing infection and infection acquisition in individuals in one or more populations in an ecosystem. infection in ecosystem endemic An infectious disease control strategy that has a vector control action specification as part. William R. Hogan An infectious disease control strategy that attempts to reduce infections in a population of a particular host species by limiting infection acquisitions from a second host species, called the 'vector'. VectorControlMeasure Typically, the strategy is to limit the population of the second host species, which is called the "vector" for the infection. vector control strategy A census of entities of a certain type or types in the abiotic ecosystem. William R. Hogan A census of things in the abiotic ecosystem. AbioticThingCensus abiotic ecosystem census An action specification that is realized in reducing the number of infection acquistions in one population of a particular species from infectious hosts in a population of another particular species, called the "vector". William R. Hogan An action specification that is realized in reducing the number of infection acquistions in one population of a particular species from infectious hosts in a population of another particular species, called the "vector". vector control action specification The average number of water containers testing positive for the presence of a particular mosquito species, typically Aedes aegyptii, per 100 households in the geographical region under surveillance. William R. Hogan The average number of containers positive (for presence of mosquito) per 100 households. breteauIndex Breteau Index A multicellular organism reproduction that has as its agent a mosquito (taxon Culicidae, ID 7157) William R. Hogan Reproduction of a single mosquito MosquitoReproduction individual mosquito reproduction The duration of the temporal interval occupied by a gonotropic period. Matthew Diller William R. Hogan The duration of the gonotrophic cycle in a female mosquito. gonotrophicPeriodDuration gonotrophic cycle duration The process in a female mosquito of taking a blood meal, developing eggs, and laying the eggs (oviposition). William R. Hogan The process in a female mosquito of taking a blood meal, developing eggs, and laying the eggs (oviposition). gonotrophic cycle An abiotic ecosystem census of the locations where pregnant female mosquitos lay their eggs. William R. Hogan A census of sites where mosquitoes have laid their eggs. OvipositionSiteCensus oviposition site census William R. Hogan The maximum number of ovisites in/around a single house or other dwelling structure. carryingCapacityPerHouse obsolete carrying capacity per house true A process that is part of an infectious disease course, has the same beginning temporal boundary as the disease course, and has an ending temporal boundary at the onset of symptoms due to the infectious disease. William R. Hogan The period from onset of infection to onset of symptoms. incubationPeriod incubation period A treatment with a drug product. William R. Hogan Treatment with a drug. DrugTreatment drug treatment An infectious disease control strategy whereby the household members of infectious indivduals voluntarily stay at home to avoid further potentially infectious contacts. William R. Hogan An infectious disease control strategy whereby the household members of infectious indivduals voluntarily stay at home to avoid further potentially infectious contacts. VoluntaryHouseholdQuarantineControlMeasure voluntary household quarantine control strategy An infectious disease conrol straegy that seeks to reduce disease transmission by offering employees extra paid time off to stay home, in an attempt to reduce contacts that transmit disease in the workplace. William R. Hogan An infectious disease conrol straegy that seeks to reduce disease transmission by offering employees extra paid time off to stay home, in an attempt to reduce contacts that transmit disease in the workplace. LiberalSickLeaveControlMeasure liberal sick leave control strategy epidemic investigation study design William R. Hogan A study design that specifies which epidemic(s) to investigate, how, and what information to output. epidemic investigation design quarantine control strategy William R. Hogan An infectious disease control strategy whereby organisms who have had contact with infectious organisms but are not symptomatic or otherwise known to be infectious are prevented from having contact with other susceptible organisms. quarantine control strategy A vector control strategy that has an action specification that is realized by reducing the number of larval-stage organisms of a vector population. Matthew Diller William R. Hogan A vector control strategy that kills larval-stage vector organisms LarvicideControlMeasure larvicide control strategy biological colonization a reproduction of a pathogen of a particular biological taxon inside a host organism of another taxon, without invasion of the tissues of the host. William R. Hogan a reproduction of a pathogen of a particular biological taxon inside a host organism of another taxon, without invasion of the tissues of the host. Colonization Primary use case is colonization of humans, animals with Staph aureus, but it also covers bacteriuria, transient bactermia, and normal gut flora. colonization infection in a population an infection in an ecosystem occurring in one population of organisms William R. Hogan an infection in an ecosystem occurring in one population of organisms Infection infection in population colonization acquisition a biological process where a pathogen organism of a particular biological taxon enters into a host organism of a particular taxon and begins to undergo reproduction in a location external to tissues of the host William R. Hogan a biological process where a pathogen organism of a particular biological taxon enters into a host organism of a particular taxon and begins to undergo reproduction in a location external to tissues of the host ColonizationAcquisition the host organism was not colonized wtih the pathogen prior to the colonization acquisition colonization acquisition decolonization control strategy an indivdiual treatment control strategy that prevents infectious disease by treating indivdiuals colonized with a pathogen of a particular species to limit or end the colonization William R. Hogan an indivdiual treatment control strategy that prevents infectious disease by treating indivdiuals colonized with a pathogen of a particular species to limit or end the colonization DecolonizationControlMeasure typically the pathogen is a bacterium decolonization control strategy establishment of infection from self colonization An infection acquisition by which a pathogen organism from a particular biological taxon, which previously was participating in a colonization process in a host organism from another taxon, begins to invade the tissues of the same host organism and reproduce there. William R. Hogan An infection acquisition by which a pathogen organism from a particular biological taxon, which previously was participating in a colonization process in a host organism from another taxon, begins to invade the tissues of the same host organism and reproduce there. infection acquistion from self colonization chemical resistance to infection A resistance to infection that is conferred by the presence, in sufficient quantity, of a particular molecular entity that is not normally present in the organism. William R. Hogan chemoprotection chemoprotective resistance chemotherapeutic resistance to infection A resistance to infection that is conferred by the presence, in sufficient quantity, of a particular molecular entity that is not normally present in the organism. As with all dispositions, chemical resistance need not be realized to exist. The presence of cholorquine confers this disposition even if the person is never bitten by a mosquito, let alone a malaria-laden mosquito. Examples: chemoprophylaxis of malaria with chloroquine, treatment of infections with antibiotics, antiviral treatment chemical resistance to infection resistance to malaria infection A resistance to infection by P. vivax, P. ovale, P. malariae, and/or P. falciparum. William R. Hogan malaria resistance resistance to malaria A resistance to infection by P. vivax, P. ovale, P. malariae, and/or P. falciparum. resistance to malaria infection A symbiosis where the organisms that are interacting remain physically external to one another. Matthew Diller William R. Hogan A symbiosis where the organisms that are interacting remain physically external to one another. It includes situations where one organism lives on the surface of the other organism. ectosymbiosis An ectosymbiosis that results in harm to all participating organisms. Matthew Diller William R. Hogan An ectosymbiosis that results in harm to all participating organisms. Example: competition between lions and hyenas for food antagonism An ectosymbiosis that results in harm to one of the participating organisms but neither harms nor benefits the other participating organisms. Matthew Diller William R. Hogan An ectosymbiosis that results in harm to one of the participating organisms but neither harms nor benefits the other participating organisms. Example: Spanish ibex and weevils of the genus Timarcha amensalism An ectosymbiosis that results in harm to one of the participating organisms and benefit to another participating organism. Matthew Diller William R. Hogan An ectosymbiosis that results in harm to one of the participating organisms and benefit to another participating organism. agonism An agonism where the participating organisms, although physically external to one another, nevertheless have close and persistent physical contact for most or all of the interaction. Matthew Diller William R. Hogan An agonism where the participating organisms, although physically external to one another, nevertheless have close and persistent physical contact for most or all of the interaction. intimate agonism An intimate agonism in which the harm is not fatal to the host. Matthew Diller William R. Hogan ectoparasitism An intimate agonism in which the harm is not fatal to the host. Example: Temnocephala chilensis and various marine wildlife ectosymbiotic parasitism An ectosymbiotic parasitism that realizes some facultative parasite role inhering in an organism that is also realized by a bodily benefit to that organism. Matthew Diller William R. Hogan facultative ectoparasitism An ectosymbiotic parasitism that realizes a disposition of the parasite that is not one of its biological functions. Example: Armillaria (type of wood fungus) and trees facultative ectosymbiotic parasitism An ectosymbiotic parasitism that realizes a biological function that inheres in some proper part of the parasite. Matthew Diller William R. Hogan obligatory ectoparasitism An ectosymbiotic parasitism that realizes a biological function that inheres in some proper part of the parasite. Example: European common cuckoo and other bird species (brood parasitism) obligatory ectosymbiotic parasitism An intimate agonism in which the harm is fatal to the host. Matthew Diller William R. Hogan ectoparasitoidism An intimate agonism in which the harm is fatal to the host. ectosymbiotic parasitoidism An ectosymbiotic parasitoidism that realizes some facultative parasitoid role inhering in an organism that is also realized by a bodily benefit to that organism. Matthew Diller William R. Hogan facultative ectoparasitoidism An ectosymbiotic parasitoidism that realizes a disposition of the parasitoid that is not one of its biological functions. Example: Pachycrepoideus dubius and Ceratitis capitata facultative ectosymbiotic parasitoidism An ectosymbiotic parasitoidism that realizes a biological function that inheres in some proper part of the parasitoid. Matthew Diller William R. Hogan obligatory ectoparasitoidism An ectosymbiotic parasitoidism that realizes a biological function that inheres in some proper part of the parasitoid. Example: Mutillidae (family of wasps) and other wasps/ants obligatory ectosymbiotic parasitoidism An ectosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms. Matthew Diller William R. Hogan ectocommensalism An ectosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms. ectosymbiotic commensalism An ectosymbiotic commensalism that realizes some facultative commensal role inhering in an organism that is also realized by a bodily benefit to that organism. Matthew Diller William R. Hogan facultative ectocommensalism An ectosymbiotic commensalism that realizes a dispostion of the organism that benefits that is not one of its biological functions. Example: Ophiodromus pugettensis and Patiria miniata facultative ectosymbiotic commensalism An ectosymbiotic commensalism that realizes a biological function that inheres in some proper part of the commensal organism that benefits. Matthew Diller William R. Hogan obligatory ectocommensalism An ectosymbiotic commensalism that realizes a biological function that inheres in some proper part of the commensal organism that benefits. Example: Basicladia algae and sea turtles obligatory ectosymbiotic commensalism An ectosymbiosis that results in benefit to all participating organisms. Matthew Diller William R. Hogan ectomutualism An ectosymbiosis that results in benefit to all participating organisms. ectosymbiotic mutualism An ectosymbiotic mutualism that realizes some facultative mutualist role inhering in an organism that is also realized by a bodily benefit to that organism. Matthew Diller William R. Hogan facultative ectomutualism An ectosymbiotic mutualism that realizes one or more dispositions of one or both organisms and these dispostions are not biological functions of either organism. Example: ants that feed off of honeydew from aphids, and in turn protect the aphids facultative ectosymbiotic mutualism An ectosymbiotic mutualism that realizes a biological function that inheres in some proper part of at least one of the organisms participating. Matthew Diller William R. Hogan obligatory ectomutualism An ectosymbiotic mutualism that realizes a biological function that inheres in some proper part of at least one of the organisms participating. Example: bees and flowers obligatory ectosymbiotic mutualism A symbiosis where one organism is physically contained within another organism (called the 'host'). Matthew Diller William R. Hogan A symbiosis where one organism is physically contained within another organism (called the 'host'). endosymbiosis An endosymbiosis that results in benefit to the parasite and harm to the host. Matthew Diller William R. Hogan endoparasitism An endosymbiosis that results in benefit to the parasite and harm to the host. endosymbiotic parasitism An agonism where the participating organisms maintain significant physical separation from one another through most or all of the interaction. Matthew Diller William R. Hogan An agonism where the participating organisms maintain significant physical separation from one another through most or all of the interaction transient agonism A non-intimate agonism in which the harm is fatal. Matthew Diller William R. Hogan A non-intimate agonism in which the harm is fatal. Example: lion and gazel predation A non-intimate agonism in which the harm is not fatal. Matthew Diller William R. Hogan A non-intimate agonism in which the harm is not fatal. Example: Giant panda and bamboo grazing An endosymbiotic parasitism that realizes some facultative parasite role inhering in an organism that is also realized by a bodily benefit to that organism. Matthew Diller William R. Hogan facultative endoparasitism An endosymbiotic parasitism that realizes a disposition of the parasite that is not one of its biological functions. Example: Strongyloides stercoralis (roundworm) and humans facultative endosymbiotic parasitism An endosymbiotic parasitism that realizes a biological function that inheres in some proper part of the parasite. Matthew Diller William R. Hogan obligatory endoparasitism An endosymbiotic parasitism that realizes a biological function that inheres in some proper part of the parasite. Example: Necator americanus (hookworm) and humans obligatory endosymbiotic parasitism An endosymbiosis that results in benefit to the parasitoid and is fatal to the host. Matthew Diller William R. Hogan endoparasitoidism An endosymbiosis that results in benefit to the parasitoid and is fatal to the host. endosymbiotic parasitoidism An endosymbiotic parasitoidism that realizes some facultative parasitoid role inhering in an organism that is also realized by a bodily benefit to that organism. Matthew Diller William R. Hogan facultative endoparasitoidism An endosymbiotic parasitoidism that realizes a disposition of the parasitoid that is not one of its biological functions. Example: Naegleria fowleri (brain-eating amoeba) and humans facultative endosymbiotic parasitoidism An endosymbiotic parasitoidism that realizes a biological function that inheres in some proper part of the parasitoid. Matthew Diller William R. Hogan obligatory endoparasitoidism An endosymbiotic parasitoidism that realizes a biological function that inheres in some proper part of the parasitoid. Example: Ichneumon eumerus (wasp) and Phengaris rebeli (butterfly caterpillar) obligatory endosymbiotic parasitoidism An endosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms. Matthew Diller William R. Hogan endocommensalism An endosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms. endosymbiotic commensalism An endosymbiotic commensalism that realizes some facultative commensal role inhering in an organism that is also realized by a bodily benefit to that organism. Matthew Diller William R. Hogan facultative endocommensalism An endosymbiotic commensalism that realizes a dispostion of the non-host organism that benefits that is not one of its biological functions. Example: Malaria and mosquito vector facultative endosymbiotic commensalism An endosymbiotic commensalism that realizes a biological function that inheres in some proper part of the commensal organism that benefits. Matthew Diller William R. Hogan obligatory endocommensalism An endosymbiotic commensalism that realizes a biological function that inheres in some proper part of the commensal organism that benefits. Example: Passalurus ambiguus (nematode) and rabbits obligatory endosymbiotic commensalism An endosymbiosis that results in benefit to all participating organisms. Matthew Diller William R. Hogan endomutualism An endosymbiosis that results in benefit to all participating organisms. endosymbiotic mutualism An endosymbiotic mutualism that realizes some facultative mutualist role inhering in an organism that is also realized by a bodily benefit to that organism. Matthew Diller William R. Hogan facultative endomutualism An endosymbiotic mutualism that realizes one or more dispositions of one or both organisms and these dispostions are not biological functions of either organism. Example: Hamiltonella defensa and aphids facultative endosymbiotic mutualism An endosymbiotic mutualism that realizes a biological function that inheres in some proper part of at least one of the organisms participating. Matthew Diller William R. Hogan obligatory endomutualism An endosymbiotic mutualism that realizes a biological function that inheres in some proper part of at least one of the organisms participating. Example: marine worms of genus Riftia and their endosymbiotic bacteria obligatory endosymbiotic mutualism A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning. Matthew Diller William R. Hogan A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning. deprecated homeostasis true A process that has as output a material entity that is the material basis for an abnormal homeostasis dispostion. Matthew Diller William R. Hogan A process that has as output a material entity that is the material basis for an abnormal homeostasis dispostion. bodily harm A process that facilitates the realization of one or more normal homeostasis dispositions borne by an organism and/or one or more causally relatively isolated parts of the organism. Matthew Diller William R. Hogan A process that facilitates the realization of one or more normal homeostasis dispositions borne by an organism and/or one or more causally relatively isolated parts of the organism. bodily benefit An organism participating in an ectosymbiotic or endosymbiotic parasitism as the organism that benefits. Matthew Diller William R. Hogan An organism participating in an ectosymbiotic or endosymbiotic parasitism as the organism that benefits. parasite An organism participating in an ectosymbiotic or endosymbiotic parasitoidism as the organism that benefits. Matthew Diller William R. Hogan An organism participating in an ectosymbiotic or endosymbiotic parasitoidism as the organism that benefits. parasitoid An information content entity that is part of an infectious disease control strategy and that specifies the intended population to which one or more interventions in the control strategy will be applied. An information content entity that is part of an infectious disease control strategy and that specifies the intended population to which one or more interventions in the control strategy will be applied. TargetPopulationDefinition target population definition A name of temporal region that designates a temporal boundary Matthew Diller William R. Hogan An information content entity that designates a temporal boundary RealTimePointCategoryDefinition name of a temporal boundary An information content entity that specifies a geographical region by (1) listing the names of other geographical regions whose mereological sum constitutes it and optionally (2) listing the names of other geographical regions that are subsequently subtracted from the mereological sum. Matthew Diller William R. Hogan An information content entity that specifies a geographical region by (1) listing the names of other geographical regions whose mereological sum constitutes it and optionally (2) listing the names of other geographical regions that are subsequently subtracted from the mereological sum. LocationDefinition location definition A contraindication that increases the risk of a treatment. Matthew Diller William R. Hogan A contraindication that increases the risk of a treatment. TreatmentContraindication treatment contraindication A duration that is specified as a probability distribution over a range of numbers. Matthew Diller William R. Hogan A duration that is specified as a probability distribution over a range of numbers. UncertainDuration uncertain duration A measurement datum that is the fraction of things of a particular type in a particular geographical region or site that are contaminated with a pathogen. Matthew Diller William R. Hogan A measurement datum that is the fraction of things of a particular type in a particular geographical region or site that are contaminated with a pathogen. fractionContaminated fraction of contaminated thing specificity of case detection The specificity of a system that classifies organisms into the binary categories of individual who meets the criteria of a particular case definition and individual who does NOT meet the criteria of a particular type of disease X. William R. Hogan The specificity of a process or system that detects organisms who satisfy a case definition. specificityOfCaseDetection specificity of case detection The specificity of a system that classifies organisms into the binary categories of having received a particular treatment and not having received a particular treatment. William R. Hogan The specificity of the process or system that detects organisms that have undergone a particular treatment. specificityOfTreatmentDetection specificity of treatment detection The sensitivity of a system that classifies organisms into the binary categories of having received a particular treatment and not having received a particular treatment. William R. Hogan The sensitivity of the process or system that detects organisms that have undergone a particular treatment. sensitivityOfTreatmentDetection sensitivity of treatment detection A duration that is specified as a single number. A duration that is specified as a single number. FixedDuration fixed duration RealTimeSpanCategoryDefinition real time span category definition RealDateSpanCategoryDefinition real date span category definition An objective specification to observe and/or estimate all the organisms of a particular taxon in a particular geographical region or place and create a data set about them. Matthew Diller William R. Hogan An objective specification to observe all the organisms of a particular taxon in a particular geographical region or place and create a data set about them. Today, census taking typically consist of some mixture of counting the number of individuals in a population and estimating the numbers of subpopulations that are prone to overcounting or undercounting. census objective specification A plan specification with a census objective specification. Matthew Diller William R. Hogan A plan specification with a census objective specification. census plan specification A planned process that realizes a census plan specification. Matthew Diller William R. Hogan A planned process that realizes a census plan specification. Census census taking A vector control strategy that is realized by releasing individuals of the vector population infected with bacteria of the taxon Wolbachia to inhibit reproduction of individuals in the vector population. Matthew Diller William R. Hogan A vector control strategy that is realized by releasing individuals of the vector population infected with bacteria of the taxon Wolbachia to inhibit reproduction of individuals in the vector population. WolbachiaControlStrategy Wolbachia vector control strategy A vector control strategy that is realized by spraying chemicals in a place to kill individuals of the vector population. Matthew Diller William R. Hogan A vector control strategy that is realized by spraying chemicals in a place to kill individuals of the vector population. IndoorResidualSprayingVectorControlMeasure indoor residual spraying vector control strategy A vector control strategy for mosquitoes that is realized by reducing the number of water-containing vessels in which mosquitoes can lay eggs. Matthew Diller William R. Hogan A vector control strategy for mosquitoes that is realized by reducing the number of water-containing vessels in which mosquitoes can lay eggs. ContainerReductionControlMeasure container reduction vector control strategy An information content entity that specifies how many doses or courses of treatment, per a particular unit of time (typically one day), can be supplied for a given geographical region and/or how many of those doses or courses can subsequently be administered. Matthew Diller William R. Hogan An information content entity that specifies how many doses or courses of treatment, per a particular unit of time (typically one day), can be supplied for a given geographical region and/or how many of those doses or courses can subsequently be administered. TreatmentSystemLogistics treatment system logistics A disposition of a treatment surveillance infrastructure to detect individuals who have received treatment in the geographical region the infrastructure aims to cover. Matthew Diller William R. Hogan A disposition of a treatment surveillance infrastructure to detect individuals who have received treatment in the geographical region the infrastructure aims to cover. TreatmentSurveillanceCapability treatment surveillance capability name of temporal region A population survey that assesses the presence (plus or minus quantity) of antibody to a particular antigen in individuals in a population. Matthew Diller William R. Hogan A population survey that assesses the presence (plus or minus quantity) of antibody to a particular antigen in individuals in a population. PopulationSerologySurvey population serology survey A data set that is a collection of case records. Matthew Diller William R. Hogan A data set that is a collection of case records. CaseList infection case list 1 A data set whose data items are about a host and its participation in an infection and potentially other activities occuring in the same time interval as the infection. Matthew Diller William R. Hogan A data set whose data items are about a host and its participation in an infection and potentially other activities occuring in the same time interval as the infection. CaseRecord infection case record A count of individuals in a population who meet an infection case definition during a particular time interval. Matthew Diller William R. Hogan A count of individuals in a population who meet an infection case definition during a particular time interval. deprecated infection case count true The temporal interval occupied by an epidemic. Matthew Diller epidemic period The temporal interval occupied by an epidemic. EpidemicPeriod epidemic interval An individual behavior of a mosquito (organism of family Culicidae). Matthew Diller William R. Hogan An individual behavior of a mosquito (organism of family Culicidae). MosquitoBehavior individual mosquito behavior An individual behavior of a human being. Matthew Diller William R. Hogan An individual behavior of a human being. HumanBehavior individual human behavior A data structure that represents, for a particular infection in ecosystem, a subset of infected organisms and for each infected organism in the subset except the first one infected temporally, its infection acquisition from an infected host as a machine-readable link to that infected host. Matthew Diller William R. Hogan A data structure that represents, for a particular infection in ecosystem, a subset of infected organisms and for each infected organism in the subset except the first one infected temporally, its infection acquisition from an infected host as a machine-readable link to that infected host. TransmissionTree Because a set A is a subset of itself, we capture the possibility that all infected organisms in the epidemic are represented in the tree. This definition allows for multiple trees in an epidemic because we did not require that the first case infected temporally be the index case, although the ideal situation is that there is one tree for the epidemic that includes the index case. transmission tree infectious disposition A disposition inhering in an organism of a particular biological taxon that is realized only by the organism participating in an infection as the reproducing organism inside another organism of a different particular biological taxon. William R. Hogan A disposition inhering in an organism of a particular biological taxon that is realized only by the organism participating in an infection as the reproducing organism inside another organism of a different particular biological taxon. The disposition of Influenza A virus H3N2 subtype to infect human beings, the disposition of Plasmodium vivax to infect mosquitos and humans, the disposition of foot and mouth disease virus to infect cloven-hooved animals (sheep, cows, pigs, etc.). infectiousness potentially infectious contact process A biological process that brings the organism into sufficiently close physical proximity to a pathogen population, either in or on a contaminated thing or an infectious host, such that the organism is likely but not certain to acquire an infection with the pathogen. William R. Hogan potentially infectious contact A biological process that brings the organism into sufficiently close physical proximity to a pathogen population, either in or on a contaminated thing or an infectious host, such that the organism is likely but not certain to acquire an infection with the pathogen. potentially infectious contacting potentially infectous contact role A role borne by an organism that is realized in a potentially infectious contact process. William R. Hogan contact role infectious contact role A role borne by an organism that is realized in a potentially infectious contact process. The organism bearing this role is the organism at risk for acquiring an infection when the role is realized. Also, this role differentiates participants in a process when there are two organisms participating, so it only begins to exist during its realization, justifying its existential restriction. potentially infectious contact role potentially infectious contact organism An organism that is the bearer of a potentially infectious contact role during a potentially infectious contact process. William R. Hogan An organism that has been exposed to a pathogen by coming into close physical proximity with either an infectious host or a contaminated thing. contacted organism potentially infectious contact definition An information content entity that specifies which kinds of processes involving an interaction between a given organism and either (1) another, potentially infectious organism or (2) a contaminated environment have a sufficiently high probability of resultling in an infection acquisition by the organism to be of interest to an outbreak investigation. William R. Hogan An information content entity that specifies which kinds of processes involving an interaction between a given organism and either (1) another, potentially infectious organism or (2) a contaminated environment have a sufficiently high probability of resultling in an infection acquisition by the organism to be of interest to an outbreak investigation. ContactDefinition contact definition An individual treatment control strategy that immediately targets individuals in the population who are at the perimeter of an epidemic. Matthew Diller William R. Hogan An individual treatment control strategy that immediately targets individuals in the population who are at the perimeter of an epidemic. RingIndividualTreatmentControlMeasure ring individual treatment control strategy A seed site for a Wolbachia control measure. Matthew Diller William R. Hogan A site that is the bearer of a role which is realized by the release of Wolbachia-infected mosquitos. wolbachiaReleaseSites Wolbachia release site A vector release site action specification for a Wolbachia control measure. Matthew Diller William R. Hogan A vector control action specification that specifies the location of Wolbachia release sites according to some predetermined spatial interval. wolbachiaSitesEveryNth Wolbachia every nth site release action specification The rate at which offspring of the Wolbachia-infected female mosquito subpopulation (of the overall mosquito population) are not infected with Wolbachia. Matthew Diller William R. Hogan The rate at which offspring of the Wolbachia-infected female mosquito subpopulation (of the overall mosquito population) are not infected with Wolbachia. wolbachiaEffectOnLeakageRate leakage rate of Wolbachia infection in mosquito population infected with Wolbachia The rate at which bites of mosquitoes infected with both Wolbachia and a particular pathogen such as dengue result in an infection in a susceptible human host. Matthew Diller William R. Hogan The rate at which bites of mosquitoes infected with both Wolbachia and a particular pathogen such as dengue result in an infection in a susceptible human host. wolbachiaEffectOnVectorialCapacity transmission rate of pathogen to human from Wolbachia-infected mosquito bites A vector control strategy that is realized by reducing the number of adults in a vector population. Matthew Diller William R. Hogan A vector control strategy that is realized by reducing the number of adults in a vector population. adult vector control strategy An adult vector control strategy that is used prior to a Wolbachia vector control strategy to increase the percentage of the adult population that gets infected with Wolbachia. Matthew Diller William R. Hogan An adult vector control strategy that is used prior to a Wolbachia vector control strategy to increase the percentage of the adult population that gets infected with Wolbachia. wolbachiaPreReleaseAdultSuppressionEfficacy Wolbachia prerelease adult vector control strategy An larvicide vector control strategy that is used prior to a Wolbachia vector control strategy to increase the percentage of the population that gets infected with Wolbachia. Matthew Diller William R. Hogan An larvicide vector control strategy that is used prior to a Wolbachia vector control strategy to increase the percentage of the population that gets infected with Wolbachia. wolbachiaPreReleaseLarvalSuppressionEfficacy Wolbachia prerelease larvicide vector control strategy A data structure that refers to (1) a subpopulation of a population based on life stage, (2) the rate of mortality of that subpopulation, and (3) the average duration of time that the individuals in the subpopulation spend in that life stage. Matthew Diller William R. Hogan A data structure that refers to (1) a subpopulation of a population based on life stage, (2) the rate of mortality of that subpopulation, and (3) the average duration of time that the individuals in the subpopulation spend in that life stage. LifeStageWithDurationAndMortality life stages with duration and mortality A process of change in the egg mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population. Matthew Diller William R. Hogan A process of change in the egg mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population. wolbachiaEffectOnEggMortalityRate Wolbachia effect on egg mortality rate in mosquito population A process of change in the adult mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population. Matthew Diller William R. Hogan A process of change in the adult mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population. wolbachiaEffectOnAdultMortalityRate Wolbachia effect on adult mortality rate in mosquito population A process of change in the larval mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population. Matthew Diller William R. Hogan A process of change in the larval mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population. wolbachiaEffectOnLarvalMortalityRate Wolbachia effect on larval mortality rate in mosquito population A process of change in fecundity of females in a mosquito population that is the outcome of an infection in that population with a Wolbachia bacteria population. Matthew Diller William R. Hogan A process of change in fecundity of females in a mosquito population that is the outcome of an infection in that population with a Wolbachia bacteria population. wolbachiaEffectOnFecundity Wolbachia effect on female fecundity in mosquito population A data item that specifies both an interval estimate centered around some sample statistic, and the probability that the process/method of obtaining the interval estimate's range of values will generate an interval that contains some unobserved population parameter of interest. Matthew Diller William R. Hogan confidence interval A seed release interval for a Wolbachia control measure. Matthew Diller William R. Hogan A seed release interval for a Wolbachia control measure. wolbachiaReleaseInterval Wolbachia release interval A data structure that specifies both the sample mean and the confidence interval generated by the measurement process. Matthew Diller William R. Hogan MeanWithConfidenceInterval mean with confidence interval A data structure that specifies both the sample mean and the standard deviation generated by the measurement process. Matthew Diller William R. Hogan MeanWithStandardDeviation mean with standard deviation A vector control action specification that specifies the number of Wolbachia-infected adult mosquitoes to be released at each household for some Wolbachia control measure. Matthew Diller William R. Hogan A vector control action specification that specifies the number of Wolbachia-infected adult mosquitoes to be released at each household. wolbachiaSeedAdultsPerHouse number of Wolbachia-infected mosquitoes released per house An epidemic simulator action specification that when set to true, results in the simuator clearing each simulated Wolbachia-infected mosquito of its simulated Wolbachia infection whenever it migrates out of the simulated population location. Matthew Diller William R. Hogan An epidemic simulator action specification that when set to true, results in the simulator clearing each simulated Wolbachia-infected mosquito of its simulated Wolbachia infection whenever it migrates out of the simulated population location. clearWolbachiaOnMigration clear Wolbachia upon vector migration A predicted data item expressing the probability that a disease outcome occurs during the disease course of an organism. Matthew Diller William R. Hogan A predicted data item expressing the probability that a disease outcome occurs during the disease course of an organism. DiseaseOutcomeWithProbability disease outcome with probability A name of a temporal region that is systematized according to a particular calendar system, such as the Gregorian calendar. Matthew Diller William R. Hogan A name of a temporal region that is systematized according to a particular calendar system, such as the Gregorian calendar. date date A scalar value specification that gives the diameter in meters of the circular area around which all organisms in a population are living will receive a vaccination as part of a ring vaccination control measure. Matthew Diller William R. Hogan A scalar value specification that gives the diameter in meters of the circular area around which all organisms in a population are living will receive a vaccination as part of a ring vaccination control measure. ringDiameterInMeters ring diameter in meters An epidemic simulator actions specification that specifies the factor by which to multiply the mating probability of a male mosquito if it is infected with a Wolbachia bacterium. Matthew Diller William R. Hogan An epidemic simulator actions specification that specifies the factor by which to multiply the mating probability of a male mosquito if it is infected with a Wolbachia bacterium. wolbachiaEffectOnMatingProbability Wolbachia effect on mating probability A data item that specifies the smallest numerical value in a data set of scalar measurement data items. Matthew Diller William R. Hogan A data item that specifies the smallest numerical value in a data set of scalar measurement data items. minimumValue minimum value A data item that specifies the largest numerical value in a data set of scalar measurement data itmes. Matthew Diller William R. Hogan A data item that specifies the largest numerical value in a data set of scalar measurement data itmes. maximumValue maximum value A predicted data item that estimates how reliable some method of statistical inference will be at estimating the population parameter of interest. Matthew Diller William R. Hogan A predicted data item that estimates how reliable some method of statistical inference will be at estimating the population parameter of interest. confidence statistical confidence A one-dimensional temporal region occupied by a place closure control strategy. Matthew Diller William R. Hogan A one-dimensional temporal region occupied by a place closure control strategy. closure period true An information content entity that delimits an interval data structure based on some value that is less than or equal to all other values within that data structure. Matthew Diller William R. Hogan An information content entity that delimits an interval data structure based on some value that is less than or equal to all other values within that data structure. lowerBound lower bound A measurement datum that is the fraction of a particular adult vector population that have undergone 1) infection acquisition with a pathogen, and 2) have experienced some outcome of the resulting infection. Matthew Diller William R. Hogan A measurement datum that is the fraction of a particular adult vector population that have undergone 1) infection acquisition with a pathogen, and 2) have experienced some outcome of the resulting infection. fractionOfVectorIndividualsAffected fraction of vector adults affected A measurement datum that is the fraction of eggs laid by a particular host population that has been destroyed and thus will not develop into a new member of the population. Matthew Diller William R. Hogan A measurement datum that is the fraction of eggs laid by a particular host population that has been destroyed and thus will not develop into a new member of the population. fractionReductionOfEggs fraction reduction of eggs A measurement datum that is the fraction of the larval subpopulation of a particular host population that has died due to some event in the population (e.g, due to a particular control measure). Matthew Diller William R. Hogan A measurement datum that is the fraction of the larval subpopulation of a particular host population that has died due to some event in the population (e.g, due to a particular control measure). fractionReductionOfLarvae fraction reduction of larvae A length measurement datum that specifies the radius of a circle, which is centered at a vector organism, for which there is a certain probability that the vector organism will bite a susceptible host. Matthew Diller William R. Hogan A length measurement datum that specifies the radius of a circle, which is centered at a vector organism, for which there is a certain probability that the vector organism will bite a susceptible host. biteRadius vector bite radius A duration that measures the temporal interval between some vector bite n and some vector bite n+1. Matthew Diller William R. Hogan A duration that measures the temporal interval between some vector bite n and some vector bite n+1. timeBetweenBites time between vector bites A rate measurement datum of that divides the total distance traveled during some migration process by the duration of the temporal interval occupied by that process. Matthew Diller William R. Hogan A rate measurement datum of that divides the total distance traveled during some migration process by the duration of the temporal interval occupied by that process. migrationSpeed migration speed An information content entity that specifies the probability that a given mosquito will realize a disposition to seek out a shaded environment when it isn't seeking a host or ovisite. Matthew Diller William R. Hogan An information content entity that specifies the probability that a given mosquito will realize a disposition to seek out a shaded environment when it isn't seeking a host or ovisite. shadeAffinity shade affinity A rate measurement datum that specifies the ratio of distance travelled during a movement process to the duration of the time interval occupied by the process. Matthew Diller William R. Hogan A rate measurement datum that specifies the ratio of distance travelled during a movement process to the duration of the time interval occupied by the process. speedOfMovement movement speed A rate measurement datum that specifies the percentage of organisms within a population that have died over a given time interval. Matthew Diller William R. Hogan A rate measurement datum that specifies the percentage of organisms within a population that have died over a given time interval. mortalityRate mortality rate A data item that specifies, as a ratio, the total count of oviposition sites located externally to all places in a geographic region relative to the total count of oviposition sites located internally to some place in that geographic region. Matthew Diller William R. Hogan A data item that specifies, as a ratio, the total count of oviposition sites located externally to all places in a geographic region relative to the total count of oviposition sites located internally to some place in that geographic region. ratioOfOutdoorToIndoorOvisites ratio of outdoor to indoor ovisites An information content entity that delimits an interval data structure based on some value that is greater than or equal to all other values within that data structure. Matthew Diller William R. Hogan An information content entity that delimits an interval data structure based on some value that is greater than or equal to all other values within that data structure. upperBound upper bound A data item that specifies the dispersion of values around some parameter in a set of data, and whose values are standardized to express the same unit of measure as the parameter of interest. Matthew Diller William R. Hogan σ A data item that specifies the dispersion of values around some parameter in a set of data, and whose values are standardized to express the same unit of measure as the parameter of interest. standardDeviation standard deviation The duration of some process wherein one or more potentially infectious contact organisms (i.e., contacted organisms) are under physical isolation from other organisms within a population. Matthew Diller William R. Hogan The duration of some process wherein one or more potentially infectious contact organisms (i.e., contacted organisms) are under physical isolation from other organisms within a population. quarantinePeriod quarantine period The probability that some male mosquito and some female mosquito within a certain distance of each other realize some disposition to reproduce with one another. Matthew Diller William R. Hogan The probability that some male mosquito and some female mosquito within a certain distance of each other realize some disposition to reproduce with one another. matingProbability mosquito mating probability An information content entity that specifies the probability that a given mosquito realizes some disposition to seek out a building if it isn't seeking a host or ovisite. Matthew Diller William R. Hogan An information content entity that specifies the probability that a given mosquito realizes some disposition to seek out a building if it isn't seeking a host or ovisite. buildingAffinity affinity for buildings An epidemic simulator action specification that specifies the linear distance a female mosquito will travel to find the next oviposition site after depositing some of its eggs at the previous one. Matthew Diller William R. Hogan An epidemic simulator action specification that specifies the linear distance a female mosquito will travel to find the next oviposition site after depositing some of its eggs at the previous one. straightTravelAfterOviposit linear distance travelled between oviposits An average value that specifies the number of eggs produced during one reproductive cycle for each individual female within a population. Matthew Diller William R. Hogan An average value that specifies the number of eggs produced during one reproductive cycle for each individual female within a population. eggsPerBrood eggs per brood A disposition of an organism to (i) undergo some bodily benefit that (ii) is triggered by a planned process. Matthew Diller William R. Hogan A disposition of an organism to (i) undergo some bodily benefit that (ii) is triggered by a planned process. efficacy We often say in natural language it is the efficacy of the triggering planned process such as vaccination. However, processes do not have properties such as roles, dispositions, functions, qualities in BFO. And this is also not a process profile, because it is not the process of a quality changing values (determinates) over time. Nevertheless, it is natural to classify efficacies based on the type of triggering process because that is what differentiates what happens when they are realized. For example, a vaccination efficacy will be realized through different processes than a quarantine efficacy. For individual treatments, the triggering process is a treatment (as defined by OGMS). efficacy A temporal part of a disease course that itself has a temporal part of becoming symptomatic, followed by another temporal part that is characterized by the organism experiencing mild, non-disease-specific symptoms. Matthew Diller William R. Hogan A temporal part of a disease course that itself has a temporal part of becoming symptomatic, followed by another temporal part that is characterized by the organism experiencing mild, non-disease-specific symptoms. prodromal period A temporal part of a disease course that 1) itself has a temporal part of becoming severely symptomatic, 2) terminates in either death or some bodily harm, and 3) has a sudden onset and short duration. Matthew Diller William R. Hogan A temporal part of a disease course that 1) itself has a temporal part of becoming severely symptomatic, 2) terminates in either death or some bodily harm, and 3) has a sudden onset and short duration. Although it is often or even typically preceded by a prodromal period, it is not always the case. Therefore "immediately preceded by some prodromal period" cannot be a necessary condition. fulminant period The probablity that a female mosquito feeds on or probes the host given an interaction between the mosquito and the host that brings them within a certain proximity (the bite radius). Matthew Diller William R. Hogan The probability that a female mosquito feeds on or probes the host given an interaction between the mosquito and the host that brings them within a certain proximity (the bite radius). biteProbability vector bite probability A length measurement datum that specifies the radius of a circle, which is centered at a male vector organism, for which there is some probability that it will mate with a female mosquito. Matthew Diller William R. Hogan A length measurement datum that specifies the radius of a circle, which is centered at a male vector organism, for which there is some probability that it will mate with a female mosquito. maleMatingRadius male mosquito mating radius A length measurement datum that specifies the radius of a circle that defines the geographical region in which some infectious disease control strategy will be implemented. Matthew Diller William R. Hogan A length measurement datum that specifies the radius of a circle that defines the geographical region in which some infectious disease control strategy will be implemented. coverRadius infectious disease control strategy cover radius A taxonomy identifier curated by the NCBI taxonomy database that specifies the taxonomic classification of some organism that is the recipient of some treatment. Matthew Diller William R. Hogan An identifier curated by the NCBI taxonomy database that specifies the taxonomic classification of some organism that is the recipient of some treatment. speciesOfTreatedOrganism species of treated organism An identifier that denotes a drug product. Matthew Diller William R. Hogan An identifier that denotes a drug product. drugId drug identifier A data structure that holds the mean, median, minimum value, and maximum value of one set of measurement data. Matthew Diller William R. Hogan A data structure that holds the mean, median, minimum value, and maximum value of one set of measurement data. MeanMedianMinimumMaximum mean median minimum maximum summary statistics data structure A conditional specification for some epidemic simulator that is triggered by a Boolean value that, if true, specifies that there is a non-uniform distribution of oviposition site carrying capacities in a simulated vector population. Matthew Diller William R. Hogan A conditional specification for some epidemic simulator that is triggered by a Boolean value that, if true, specifies that there is a non-uniform distribution of oviposition site carrying capacities in a simulated vector population. heterogenousCarryingCapacity heterogenous carrying capacity A site that is the bearer of a role that is realized by the release of artificially-infected vectors for the purpose of infecting the local vector population with a certain pathogen. Matthew Diller William R. Hogan A site that is the bearer of a role that is realized by the release of artificially-infected vectors for the purpose of infecting the local vector population with a certain pathogen. Class was originally created to correspond with an element from Apollo XSD v3.1.0. seed site A vector control action specification that is realized by releasing artificially-infected vector organisms at the specified time intervals. Matthew Diller William R. Hogan A vector control action specification that is realized by releasing artificially-infected vector organisms at the specified time intervals. Class was originally created to correspond with an element from Apollo XSD v3.1.0. seed release interval A vector control action specification that specifies the location of vector release sites according to some predetermined spatial interval. Matthew Diller William R. Hogan A vector control action specification that specifies the location of vector release sites according to some predetermined spatial interval. Class was originally created to correspond with an element from Apollo XSD v3.1.0. vector release site action specification A vector control action specification that specifies the number of artificially-infected vectors to be released at each household. Matthew Diller William R. Hogan A vector control action specification that specifies the number of artificially-infected vectors to be released at each household. Class was originally created to correspond with an element from Apollo XSD v3.1.0. number of artificially-infected vectors released per house An epidemic simulator action specification that, when set to true, results in the simulator clearing each simulated artificially-infected vector of its simulated infection whenever it migrates out of the simulated population location. Matthew Diller William R. Hogan An epidemic simulator action specification that, when set to true, results in the simulator clearing each simulated artificially-infected vector of its simulated infection whenever it migrates out of the simulated population location. Class was originally created to correspond with an element from Apollo XSD v3.1.0. clear infection upon vector migration An identifier curated by IHTSDO that refers to some representational unit within its class hierarchy. Matthew Diller William R. Hogan An identifier curated by IHTSDO that refers to some representational unit within its class hierarchy. SnomedId SNOMED concept identifier A data item that is about a proposition and has a numeric value between 0 and 1, inclusive, that is the output of some process of inference, such that 1) logical falsehoods and logical truths are assigned a value of 0 and 1, respectively, while contingent propositions are assigned some intermediate value; and 2) the process of inference conforms with rules for the calculation of probabilities, and that any interpretation of probability must specify the extent to which probabilities might be used to constrain the degrees of belief of rational agents. Matthew Diller William R. Hogan A data item that is about a proposition and has a numeric value between 0 and 1, inclusive, that is the output of some process of inference, such that 1) logical falsehoods and logical truths are assigned a value of 0 and 1, respectively, while contingent propositions are assigned some intermediate value; and 2) the process of inference conforms with rules for the calculation of probabilities, and that any interpretation of probability must specify the extent to which probabilities might be used to constrain the degrees of belief of rational agents. Probability The first criterion is derived from Kolmogorov's Probability Calculus, while the second is derived from Salmon's Admissibility and Applicability Criteria of Adequacy. Salmon's ascertainability criterion is subsumed by the definition for 'data item'. probability An epidemic simulator action specification that specifies the minimum number of eggs that any simulated female mosquito will oviposit during a gonotrophic cycle. Matthew Diller William R. Hogan An epidemic simulator action specification that specifies the minimum number of eggs that any simulated female mosquito will oviposit during a gonotrophic cycle. minimumEggsPerOviposition minimum eggs per oviposition site A rate measurement datum that measures the percentage decrease per unit time (typically per day) in the number of offspring to which a female mosquito passes an infection with a particular pathogen (e.g., Wolbachia). Matthew Diller William R. Hogan A rate measurement datum that measures the percentage decrease per unit time (typically per day) in the number of offspring to which a female mosquito passes an infection with a particular pathogen (e.g., Wolbachia). ageDependentFecundityReduction age-dependent fecundity reduction An epidemic simulator action specification that specifies the maximum number of larvae that can exist across all ovisites in a given house. Matthew Diller William R. Hogan An epidemic simulator action specification that specifies the maximum number of larvae that can exist across all ovisites in a given house. carryingCapacityPerHouse Mosquitos can sense eggs in ovisite so tend to lay in places not at max. carrying capacity per house An epidemic simulator action specification that specifies the comparison operation to use to determine whether some value, relative to a threshold, is one that should trigger the implementation of a control measure. Matthew Diller William R. Hogan An epidemic simulator action specification that specifies the comparison operation to use to determine whether some value, relative to a threshold, is one that should trigger the implementation of a control measure. reactiveControlMeasureOperator reactive control measure operator A time measurement datum of the length of the temporal interval occupied by a gonotropic period. Matthew Diller William R. Hogan A time measurement datum of the length of the temporal interval occupied by a gonotropic period. gonotrophic period duration true A textual entity that specifies characteristics of some entity. Matthew Diller William Hogan A textual entity that specifies characteristics of some entity. description description A probability distribution where the probability of each outcome is the range of a function (whose domain is the outcomes) that is calculated using one or more constant values (called parameters). Matthew Diller William R. Hogan A probability distribution where the probability of each outcome is the range of a function (whose domain is the outcomes) that is calculated using one or more constant values (called parameters). ParametricProbabilityDistribution parametric probability distribution A vector control strategy that has 1) an action specification that is realized in releasing artificially-infected vector organisms into a vector population, and 2) an objective specification of spreading this infection throughtout the vector population. Matthew Diller William R. Hogan A vector control strategy that has 1) an action specification that is realized in releasing artificially-infected vector organisms into a vector population, and 2) an objective specification of spreading this infection throughtout the vector population. Class was originally created to correspond with a complex type from Apollo XSD v3.1.0. seed infections into vector population control measure A predicted data item that is the maximum value of larvae that some ovisite is capable of sustaining. Matthew Diller William R. Hogan A predicted data item that is the maximum value of larvae that some ovisite is capable of sustaining. ovisite carrying capacity A behavior of one or more organisms that is characterized by the displacement from one geographic region to some target geographic region, and is the realization of either a biological function or (a concretization of) an objective specification. Matthew Diller William R. Hogan A behavior of one or more organisms that is characterized by the displacement from one geographic region to some target geographic region, and is the realization of either a biological function or (a concretization of) an objective specification. geographical movement of organism An action specification that delineates some minimum value or maximum value for some test statistic within a continuous probability distribution that is meant to serve as a lower bound or upper bound, respectively, for some population or sample of interest. Matthew Diller William R. Hogan An action specification that delineates some minimum value or maximum value for some test statistic within a continuous probability distribution that is meant to serve as a lower bound or upper bound, respectively, for some population or sample of interest. cutTailAt cut-off point specification A duration that measures a temporal region occupied by a prodromal period. Matthew Diller William R. Hogan prodromal period duration A duration that measures a temporal region occupied by a fulminant period. Matthew Diller William R. Hogan fulminant period duration A taxonomy identifier curated by the NCBI taxonomy database that has been used to specify the species of some organism in which some disease has been realized. Matthew Diller William R. Hogan An identifier curated by the NCBI taxonomy database that has been used to specify the species of some organism in which some disease has been realized. speciesWithDiseasae identifier of species of diseased organism A taxonomy identifier curated by the NCBI taxonomy database that has been used to identify the species of some organism that meets a case definition. Matthew Diller William R. Hogan An identifier curated by the NCBI taxonomy database that has been used to identify the species of some organism that meets a case definition. speciesOfCase identifier for species of case infectious disease control strategy to prevent infection acquisition by individuals traveling from one ecosystem to another ecosystem An infectious disease control strategy that has an objective specification of preventing infection acquisition by organisms traveling from one ecosystem to another ecosystem. William R. Hogan An infectious disease control strategy that has an objective specification of preventing infection acquisition by organisms traveling from one ecosystem to another ecosystem. travel-related infectious disease control strategy travel recommendation infectious disease control strategy A travel-related infectious disease control strategy that has an action specification that is realized by making recommendations to travelers to either (1) avoid travel to an ecosystem with an ongoing infection such as an epidemic, (2) take precautions when traveling to such an ecosystem, (3) receive certain vaccinations prior to traveling to such an ecosystem, or (4) take certain medications when traveling to such an ecosystem William R. Hogan A travel-related infectious disease control strategy that recommends to travelers to either (1) avoid travel to a region with an ongoing infection such as an epidemic, (2) take precautions when traveling to such a region, (3) receive certain vaccinations prior to traveling to such a region, or (4) take certain medications when traveling to such a region travel recommendation control strategy A case isolation control measure that has an action specification that is realized in preventing one or more infectious organisms from having physical contact with other organisms. Matthew Diller William R. Hogan A case isolation control measure that has an action specification that is realized in preventing one or more infectious organisms from having physical contact with other organisms. ContactIsolationControlMeasure contact isolation control measure A duration that measures the temporal interval occupied by some colonization. Matthew Diller William R. Hogan A duration that measures the temporal interval occupied by some colonization. colonizationDuration colonization duration A taxonomy identifier curated by the National Center for Biotechnology Information that specifies the taxonomic classification of some population of organisms. Matthew Diller William R. Hogan An identifier curated by the National Center for Biotechnology Information that specifies the taxonomic classification of some population of organisms. populationSpecies identifier of species of population An identifier curated by the National Library of Medicine as a unique string of integer numerals to be used as a standard way of denoting each concept in the RxNorm terminology. Matthew Diller William R. Hogan An identifier curated by the National Library of Medicine as a unique string of integer numerals to be used as a standard way of denoting each concept in the RxNorm terminology. RxNormId RxNorm drug concept identifier An identifier curated by the Regenstrief Institute to be used as a standard way of denoting each term in the LOINC database. Matthew Diller William R. Hogan An identifier curated by the Regenstrief Institute to be used as a standard way of denoting each term in the LOINC database. LoincId LOINC identifier A LOINC identifier that refers to some clinical laboratory test conducted in a particular context.. Matthew Diller Willliam R. Hogan A LOINC identifier that refers to some clinical laboratory test conducted in a particular context.. testLoincId laboratory test LOINC identifier An identifier curated by the United States National Library of Medicine and National Institutes of Health that denotes some publication record in the MEDLINE database. Matthew Diller William R. Hogan An identifier curated by the United States National Library of Medicine and National Institutes of Health that denotes some publication record in the MEDLINE database. pubMedId PubMed identifier An identifier curated by ORCID, Inc. to denote some academic author. Matthew Diller William R. Hogan An identifier curated by ORCID, Inc. to denote some academic author. http://purl.obolibrary.org/obo/IAO_0000708 orcId ORCID true A count of individuals in a population who meet the criteria of some case definition during some time interval. Matthew Diller William R. Hogan A count of individuals in a population who meet the criteria of some case definition during some time interval. CaseCount count of disease cases A count of disease cases in an infected population that meet the case definition criteria within a particular epidemic interval. Matthew Diller William R. Hogan A count of disease cases in an infected population that meet the case definition criteria within a particular epidemic interval. EpidemicCaseCounts count of cases in an epidemic An adult vector control strategy that has 1) an action specification that is realized by the use of insecticide-treated nets within households, and 2) an objective specification that is realized by preventing potentially infectious contacting between some mosquito vector and some human host. Matthew Diller William R. Hogan An adult vector control strategy that has 1) an action specification that is realized by the use of insecticide-treated nets within households, and 2) an objective specification that is realized by preventing potentially infectious contacting between some mosquito vector and some human host. InsecticideTreatedNetControlMeasure insecticide-treated net control measure A plan specification that specifies 1) the quantity of which some material entity will be allocated to the eventual realization of some action specification, and 2) the temporal regions in which each action specification is to be realized. Matthew Diller William R. Hogan A plan specification that specifies 1) the quantity of which some material entity will be allocated to the eventual realization of some action specification, and 2) the temporal regions in which each action specification is to be realized. Schedule schedule A population census about the organisms specific to that population that were the host in some colonization acquisition. Matthew Diller William R. Hogan A population census about the organisms specific to that population that were the host in some colonization acquisition. PopulationColonizationCensus population colonization census The efficacy measured for some instance(s) of drug treatment for preventing or ameliorating some disease outcome. Matthew Diller William R. Hogan The efficacy measured for some instance(s) of drug treatment for preventing or ameliorating some disease outcome. drugTreatmentEfficacy While we understand that 'drug efficacy' can have multiple interpretations, this class is specifically referring to drug efficacy in the context of clinical outcomes. As such, our definition excludes any mention of efficacy as it relates to pharmacodynamics. drug treatment efficacy A data set that comprises exactly one latitude measurement datum and exactly one longitude measurement datum as its elements, and optiionally the geodetic datum used as the coordinate system for the measurements, and each of these measurements is about the same zero-dimensional geographical region. Matthew Diller William R. Hogan A data set that comprises exactly one latitude measurement datum and exactly one longitude measurement datum as its elements, and optiionally the geodetic datum used as the coordinate system for the measurements, and each of these measurements is about the same zero-dimensional geographical region. LatLongPair latitude and longitude coordinate pair A time measurement datum that refers to the temporal interval occupied by the life course of some organism and that takes 'years' as its measurement unit label. Matthew Diller William R. Hogan A time measurement datum that refers to the temporal interval occupied by the life course of some organism and that takes 'years' as its measurement unit label. ageInYears age in years datum A duration that measures a temporal region occupied by some contamination. Matthew Diller William R. Hogan A duration that measures a temporal region occupied by some contamination. contaminationDuration contamination period duration A healthcare facility identifier that refers to some architectural structure that is the bearer of some healthcare function. Matthew Diller William R. Hogan A healthcare facility identifier that refers to some architectural structure that is the bearer of some healthcare function. healthcareFacilityId healthcare facility identifier An identifier that refers to some disease transmission model model. Matthew Diller William R. Hogan An identifier that refers to some disease transmission model model. modelId disease transmission model identifier An identifier that denotes some architectural structure. Matthew Diller William R. Hogan An identifier that denotes some architectural structure. FacilityId facility identifier An identifier that denotes a biological taxonomic group. Matthew Diller William R. Hogan taxonId taxonomy identifier An identifier that denotes an organism included in some infection case count. Matthew Diller William R. Hogan An identifier that denotes an organism included in some infection case count. caseId disease case identifier An infection acquistion from infectious host that is causally downstream of some potentially infectious sexual contacting Matthew Diller Note that infections that are acquired in this manner do not fall within the class of sexually transmitted infections (STI's), ipso facto. This type of transmission can also occur with non-STI pathogens--such as meningitis and Zika. infection acquisition through sexual activity with infectious host A rate measurement datum that is the result of the measurement of the volume of water produced by some hydrological precipitation process at a particular geographical region divided by the number of temporal intervals of equal duration over which the precipitation occurred. Matthew Diller William R. Hogan rate of hydrological precipitation An average value that takes, as input, some set of rate of hydrological precipitation data that were recorded over a particular duration of time. Matthew Diller William R. Hogan mean rate of hydrological precipitation An average value that takes, as input, some set of air temperature measurement data that were recorded over a particular duration of time. Matthew Diller William R. Hogan mean air temperature A sexual activity with at least one infectious host as participant where the infectious host(s) are infected with a pathogen that has a disposition to infect the tissues of the non-infected host that came into physical contact with the infectious host during the activity. Matthew Diller William R. Hogan potentially infectious sexual contacting host population A population of organisms some of which were susceptible to infection with a particular pathogen at some point in their lives. William R. Hogan population of host organisms host population An action specification that is part of an infectious disease control strategy that has at least one rule pertaining to some control measure. Matthew Diller William R. Hogan An action specification that is part of an infectious disease control strategy that has at least one rule pertaining to some control measure. controlMeasureNamedPrioritizationScheme prioritization scheme for control measure A data transformation that takes as its input exactly one continuous variable as a value and assesses whether any statistically significant change to that variable will produce some change to the model's output. Matthew Diller William R. Hogan A data transformation that takes as its input exactly one continuous variable as a value and assesses whether any statistically significant change to that variable will produce some change to the model's output. Class was originally created to correspond with a complex type from Apollo XSD v3.1.0. one-way sensitivity analysis of a continuous variable An identifier that is an integer numeral that denotes some citation. Matthew Diller William R. Hogan An identifier that is an integer numeral that denotes some citation. referenceId citation identifier A geographic region that contains a sampling process. Matthew Diller William R. Hogan A geographic region that contains a sampling process. whereSampled location of sampling process An infection acquisition from infectious host by an embryo, fetus, or baby from its infectious mother while in utero, in egg at any point prior to hatching (even after laying), or during childbirth. Matthew Diller William R. Hogan congenital infection acquisition infection acquisition from mother-to-child transmission An infection acquisition from infectious host by an embryo, fetus, or baby from its infectious mother while in utero, in egg at any point prior to hatching (even after laying), or during childbirth. infection acquisition from vertical transmission software source code version control repository A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc. William R. Hogan Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based source code repository process of compiling software A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions. William R. Hogan It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.). Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code. compiling software machine instructions compiled from software source code A software that is the specified output of some compilation of software process William R. Hogan compiled software code An algorithm that models some scale-free network. Matthew Diller William R. Hogan scale-free network model A graph of vertices in which, for some fraction of vertices, P(k), the number of connections, k, varies as a power of some parameter, γ. In other words, P(k) ~ k^(-γ), where 2 < γ < 3. Matthew Diller William R. Hogan scale-free network A data set that represents 1) one or more collections of organisms at some time and some geographical region; and optionally 2) the school facilities, workplace facilities, and health care facilities in that region. Matthew Diller William R. Hogan SyntheticEcosystem The interactions between each organism as they move between these facilities may also be included in the data set. synthetic ecosystem data set A probability whose value is dependent upon the occurrence, known or presumed, of some process. Matthew Diller William R. Hogan A probability whose value is dependent upon the occurrence, known or presumed, of some process. conditionalProbability conditional probability A conditional probability whose value is dependent upon the duration of some colonization or infection. Matthew Diller William R. Hogan A conditional probability whose value is dependent upon the duration of some colonization or infection. probabilityOfInfectionOverTime probability of infection over time A data item that specifies the number of susceptible organisms necessary for an epidemic to occur within a population. Matthew Diller William R. Hogan epidemic threshold A geographical migration of an organism belonging to the species Homo sapiens. Matthew Diller William R. Hogan human travel Human travel that involves 1) movement from one geographical region to another through the air as a temporal proper part, and 2) the use of some processed material (e.g., airplane, hang glider) for propulsion that has some function of mechanical flight. Matthew Diller William R. Hogan human air travel A data item that is about one or more instances of human travel, and that specifies the geographical start location, geographical end location, and the geographical regions visited throughout the process. Matthew Diller William R. Hogan human mobility data item A copyright license that is about some software and contains one or more conditional specifications that specify the use and redistribution of the software. Matthew Diller William R. Hogan A copyright license that is about some software and contains one or more conditional specifications that specify the use and redistribution of the software. software license An identifier that refers to a specific software license. Matthew Diller William R. Hogan An identifier that refers to a specific software license. SoftwareLicenseIdentification complete software license identifier An identifier that, as part of a complete software license identifier, refers to one specific version of the software license. Matthew Diller William R. Hogan An identifier that, as part of a complete software license identifier, refers to one specific version of the software license. licenseVersion software license version identifier An identifier that refers to all versions of a specific software license. Matthew Diller William R. Hogan An identifier that refers to all versions of a specific software license. licenseName software license identifier A unique resource locator that constitutes a reference to some software license. Matthew Diller William R. Hogan A unique resource locator that constitutes a reference to some software license. licenseLocation software license URL model of population dynamics software application An simulation software application that when realized simulates changes in the size and life stage distribution of a population or populations of organisms of a particular biological taxon. Matthew Diller William R. Hogan An algorithm that simulates changes in the size and life stage distribution of a population or populations of organisms of a particular biological taxon. population dynamics model disease surveillance objective specification An objective specification whose endpoint is human awareness of the level of a particular disease in a particular population of a given biological taxon during some time interval. Matthew Diller William R. Hogan An objective specification whose endpoint is human awareness of the level of a particular disease in a particular population of a given biological taxon during some time interval. disease surveillance objective specification population mortality data set A data set that is about either some mortality rate or the death events themselves of some individuals of a given population of a particular biological taxon. Matthew Diller William R. Hogan A data set that is about either some mortality rate or the death events themselves of some individuals of a given population of a particular biological taxon. mortality data pathogen evolution model software application A simulation software application that simulates the evolution over time of a particular pathogen of a particular biological taxon. Matthew Diller William R. Hogan Simulation software that simulates the evolution over time of a particular pathogen of a particular biological taxon. pathogen evolution model A planned process that is the realization of a disease surveillance objective specification. Matthew Diller William R. Hogan A planned process that is the realization of a disease surveillance objective specification. disease surveillance Individual human behavior that involves either 1) remaining in some susceptible population or some exposed population or 2) human movement away from or around an infectious population, in order to avoid being participant in some infection acquisition. Matthew Diller William R. Hogan Individual human behavior that involves either 1) remaining in some susceptible population or some exposed population or 2) human movement away from or around an infectious population, in order to avoid being participant in some infection acquisition. self-initiated travel avoidance behavior A data item that is about one or more instances of social interaction between two or more individuals, and that specifies the temporal duration of interaction, spatial distance of individuals, geographical location of individuals, and the number of individuals participant in some social behavior(s). Matthew Diller William R. Hogan A data item that is about one or more instances of social interaction between two or more individuals, and that specifies the temporal duration of interaction, spatial distance of individuals, geographical location of individuals, and the number of individuals participant in some social behavior(s). social interaction data item A compartmental disease transmission model that represents some infection in ecosystem in which there is only a susceptible population and an infectious population, such that individuals who aren't infectious are susceptible. Matthew Diller William R. Hogan A compartmental disease transmission model that represents some infection in ecosystem in which there is only a susceptible population and an infectious population, such that individuals who aren't infectious are susceptible. Susceptible-Infected-Susceptible model A compartmental disease transmission model that represents some infection in ecosystem in which there are compartments for susceptible individuals, infectious individuals, and recovered individuals, such that recovered individuals are immune to future infection. Matthew Diller William R. Hogan A compartmental disease transmission model that represents some infection in ecosystem in which there are compartments for susceptible individuals, infectious individuals, and recovered individuals, such that recovered individuals are immune to future infection. Susceptible-Infected-Resistant model An infectious disease control strategy that identifies and treats contacted organisms in a host population. Matthew Diller William R. Hogan An infectious disease control strategy that identifies and treats contacted organisms in a host population. contact tracing A compartmental disease transmission model that represents some infection in ecosystem in which there are compartments for susceptible individuals, exposed individuals, infectious individuals, and immune inviduals, such that exposed individuals are infected but cannot transmit the pathogen. Matthew Diller William R. Hogan A compartmental disease transmission model that represents some infection in ecosystem in which there are compartments for susceptible individuals, exposed individuals, infectious individuals, and immune inviduals, such that exposed individuals are infected but cannot transmit the pathogen. Susceptible-Exposed-Infectious-Recovered model A disease transmission model that is about two or more collections of organisms of a particular biological taxon in separate geographical locations and some geographical migration of organisms between them. Matthew Diller William R. Hogan A disease transmission model that is about two or more collections of organisms of a particular biological taxon in separate geographical locations and some geographical migration of organisms between them. metapopulation disease transmission model A Susceptible-Infected-Resistant model that represents exactly two infections in ecosystem by exactly two pathogens. Matthew Diller William R. Hogan A Susceptible-Infected-Resistant model that represents exactly two infections in ecosystem by exactly two pathogens. two-strain Susceptible-Infectious-Resistant model A data set that is about some disease surveillance. Matthew Diller William R. Hogan A data set that is about some disease surveillance. disease surveillance data disease transmission tree estimator software application A software application that implements an algorithm that has specified output some transmission tree. Matthew Diller William R. Hogan An algorithm that has specified output some transmission tree. disease transmission tree estimator A function inhering in some device that is realized by some movement process in the atmosphere in which the device is participant in. Matthew Diller William R. Hogan A function inhering in some device that is realized by some movement process in the atmosphere in which the device is participant in. mechanical flight function software application that forecasts disease transmission A simulation software application that has as output one or more predicted count data items that are about a host population and that predict how many infections will occur at or will have occurred at some temporal region relative to when the data items are created. Matthew Diller William R. Hogan disease forecasting software infectious disease forecasting software application infectious disease forecaster An investigation that realizes the concretization of some disease state design and that has as an occurrent part some population survey that has specified input some case definition. Matthew Diller William R. Hogan An investigation following a disease state study design that includes a population survey as part, where a case definition used in the population survey to ascertain disease state. CaseSeries case series A data set that is the output of a case series investigation. Matthew Diller William R. Hogan A data set that is the output of a case series investigation. case series data set A data set about an instance of an epidemic. Matthew Diller William R. Hogan A data set about an instance of an epidemic. epidemic data set disease transmission model software application Matthew Diller William R. Hogan disease transmission model software data format converter software application Matthew Diller William R. Hogan data format converter phylogenetic tree constructor software application A software application that implements an algorithm that has specified output a phylogenetic tree William R. Hogan phylogenetic tree constructor data visualizer software application A software application that implements an algorithm that has some data visualizer software objective specification as part. Matthew Diller William R. Hogan data visualizer computational modeling toolkit software application Matthew Diller William R. Hogan computational modeling toolkit data parsing process A data transformation that has a dataset, encoded in a particular data format specification, as input and extracts certain elements or parts of the dataset, typically into the volatile memory of a computer. William R. Hogan data reading process reading data data parsing synthetic ecosystem constructor software A software that when compiled and run, has specified output of an agent-level ecosystem data set. William R. Hogan software for creating a synthetic ecosystem dataset example: Synthia, SPEW synthetic ecosystem constructor A data item that is the output of some infection case count and that represents the number of infectious disease cases that ended in death. Matthew Diller William R. Hogan A data item that is the output of some infection case count and that represents the number of infectious disease cases that ended in death. totalFatalCaseCount total fatal disease cases A count of the total number of diseased indivduals in a population during a particular time interval. Matthew Diller William R. Hogan The total number of diseased individuals in a population at a point in time. totalCaseCount total disease cases A data item that denotes some context in which an individual realizes some employee role if he or she is a member of the labor force, or the context in which he or she is not a member of the labor force according to certain prespecified conditions. Matthew Diller William R. Hogan A data item that denotes some context in which an individual realizes some employee role if he or she is a member of the labor force, or the context in which he or she is not a member of the labor force according to certain prespecified conditions. employmentStatus If an individual is a member of the labor force, the criteria that this status is selected from includes whether they are in the armed forces, employed and working, employed but absent from work for a week, and unemployed. The criteria for those not in the labor force includes whether the individual is a houseworker, suffering from a physical impairment that prevents them from working, in school, or other miscellaneous reasons. employment status data item An abiotic ecosystem element that is participant in some biological contamination process. Matthew Diller William R. Hogan An abiotic ecosystem element that is participant in some biological contamination process. contaminatedAbioticThing contaminated abiotic thing An adult vector control strategy that has 1) an action specification that is realized by the use of mosquito traps that leverage natural or synthetic human odors as bait, and 2) an objective specification that is realized by preventing potentially infectious contacting between some mosquito vector and some human host. Matthew Diller William R. Hogan An adult vector control strategy that has 1) an action specification that is realized by the use of mosquito traps that leverage natural or synthetic human odors as bait, and 2) an objective specification that is realized by preventing potentially infectious contacting between some mosquito vector and some human host. odor-baited trap control strategy An infectious disease control strategy that attempts to prevent infection of susceptible human host organisms in a particular geographical region by increasing the population of domesticated animals in that region, such that less mosquitoes feed on humans. Matthew Diller William R. Hogan An infectious disease control strategy that attempts to prevent infection of susceptible human host organisms in a particular geographical region by increasing the population of domesticated animals in that region, such that less mosquitoes feed on humans. zoo-prophylaxis control strategy A clinical phenotype that is causally preceded by some infection or some adverse drug reaction; and that is accompanied by a fever greater than or equal to 37.8 degrees Celsius, and a cough or sore throat. Matthew Diller William R. Hogan influenza-like illness acute respiratory illness A scalar value specification whose measurement unit label is 'week' and that is part of the first predicted data item that is greater than the epidemic threshold set for that data item. Amanda Hicks Matthew Diller William R. Hogan epidemic start week A scalar value specification whose measurement unit label is 'week', and that is part of the epidemic peak intensity. Amanda Hicks Matthew Diller William R. Hogan epidemic peak week A predicted data item that is about some aggregate of cases in an epidemic and whose value specification contains the maximum value in a data set that is about the epidemic. Amanda Hicks Matthew Diller William R. Hogan epidemic peak intensity A process that (1) has as occurrent parts at least two disease courses that realize the same type of disease, and (2) has as participants two or more hosts that are members of a particular host population. Amanda Hicks Matthew Diller William R. Hogan aggregate of disease courses A planned process that realizes some infectious disease forecasting software. Matthew Diller William R. Hogan infectious disease forecast An infectious disesae forecast that realizes some infectious disease nowcasting software. Matthew Diller William R. Hogan infectious disease nowcast An objective specification that is realized by the estimation of one or more predicted data items that are about 1) some infection in ecosystem and 2) potential changes to its number of participants (e.g., individuals within a host population, individuals within a vector population) relative to a particular temporal region; and is part of some infectious disease forecasting software. Matthew Diller William R. Hogan infectious disease forecast objective specification An infectious disease forecasting objective specification that is realized by the estimation of one or more predicted data items that are about some infection in ecosystem as they are occurring in real time, and is part of some infectious disease nowcasting software. Matthew Diller William R. Hogan infectious disease nowcast objective specification infectious disease nowcasting software application An infectious disease forecasting software application that predicts how many infections are occurring within the same temporal interval that the data items are being estimated. Matthew Diller William R. Hogan infectious disease nowcaster An infectious disease forecast that has specified input some data set, the data items of which are about an infection in ecosystem that is current concomitant with the forecasting software’s executable code being realized. Matthew Diller William R. Hogan prospective infectious disease forecast An infectious disease nowcast that has specified input some data set, the data items of which are about an infection in ecosystem that is current concomitant with the forecasting software’s executable code being realized. Matthew Diller William R. Hogan prospective infectious disease nowcast An action specification that specifies the duration of time that is to elapse between each calculation of each predicted data item that is the output of some infectious disease forecast. Matthew Diller William R. Hogan infectious disease forecast time specification An inpatient encounter in which the health care provider role is realized by some person employed by the intensive care department of some health care facility, and the patient role is realized by someone admitted to that intensive care department. intensive care unit encounter An objective specification that is realized when a diagram is drawn from one or more data sets. Matthew Diller William R. Hogan data visualization objective specification treatment in the intensive care unit control strategy an individual treatment control strategy that is realized by one or more intensive care unit encounters for infected individuals in the population William R. Hogan an individual treatment control strategy that is realized by treating one or more infected individuals in an intensive care unit treatment in the ICU control strategy website that has data as a part William R. Hogan This class was created for use case for MIDAS Digital Repository to index websites that have useful data in them, albeit rarely as machine-interpretable, downloadable datasets. Much of the data are locked in PDF or other text-based formats. website with data climate data set A data set that is an aggregate of data items that are about an environmental system process (e.g., hydrological precipitation) or a participant in an environmental system process. Matt Diller William R. Hogan climate data set metagenomics analysis software application A software application that has as part an objective specification that is achieved by only a metagenomics analysis. Matthew Diller William R. Hogan metagenomics analysis software abiotic ecosystem data set A data set that is about some abiotic ecosystem or abiotic ecosystem element. William R. Hogan abiotic ecosystem dataset data set about an abiotic ecosystem or abiotic ecosystem element A data set that is about an abiotic ecosystem or some abiotic ecosystem element. abiotic ecosystem data set data set about Earth's atmosphere or some part of it A data set that is about either the Earth's atmosphere or some part of the Earth's atmosphere. William R. Hogan A data set that is about either the Earth's atmosphere or some part of the Earth's atmosphere. atmospheric data set census of treatment facility A census that counts the number of treatment facilities of some kind in a particular geographical region. William R. Hogan census of treatment facilities treatment facilities census treatment facility census A census that counts the number of treatment facilities of some kind in a particular geographical region. NOTE: this class counts the facilities themselves, not patients (people) in those facilities. For example, how many hospitals in a state. Not how many patients are in a hospital or hospitals in a state. treatment facility census symbiosis An interspecies interaction between two or more organisms in intimate association. Matthew Diller William R. Hogan Martin BD, Schwab E. Current usage of symbiosis and associated terminology. International Journal of Biology. 2013 Jan 1;5(1):32. Available from: https://web.archive.org/web/20190723160720/https://www.researchgate.net/publication/233865641_Current_Usage_of_Symbiosis_and_Associated_Terminology By "intimate interaction," we mean any interaction between two or more organisms that involves (1) physical contact or (2) multi-organism behavior in which all interacting organisms are participant. symbiosis data format validator software application A software application that takes a data set as input and outputs a determination of whether the dataset is in compliance with one or more given data format specifications. William R. Hogan data format validator disease identifier an identifier that denotes a disease. William R. Hogan Mathias Brochhausen 2021-03-16T16:01:41Z disease identifier dataset about infectious disease acquisitions The dataset at this link is rdf:type this class: https://figshare.com/articles/dataset/COVID19_settings_of_transmission_-_collected_reports_database/12173343 a dataset that is about infectious disease acquisitions at particular times and particular places. William R. Hogan 2021-03-16T16:16:26Z The dataset may include sites (e.g. types of facilities, rooms), events (e.g., church service whether in or outdoors), dates, times, geographical regions, etc. in which the sites/events are located, and so on. infection acquisition dataset dataset about hospital stays The datasets at this link are rdf:type this class: https://www.opendataphilly.org/dataset/covid-hospitalizations a dataset that is about two or more hospital stays involving two or more patients. William R. Hogan hospital discharge dataset hospitalization dataset 2021-03-16T16:20:48Z The dataset may be limited to stays in one hospital, but hospital discharge datasets as compiled by state departments of health typically contain stays from multiple hospitals (typically every hospital) in the geographical region over which they have jurisdiction hospital stay dataset human daily movement behavior an individual human behavior that is the movements from one location to another throughout the day (e.g., work, home, stores, church, relatives' homes) in the areas adjacent to where the human lives at the time. William R. Hogan 2021-03-16T16:29:53Z human daily movement human daily movement behavior data set https://www.google.com/covid19/mobility/ a data set that is about the human daily movement behavior of the individual huamns in a given population. William R. Hogan 2021-03-16T16:32:39Z human daily movement data set potentially infectious contact process data set in a population a data set that is about one or more potentially infectious contact processes in a population of host organisms. William R. Hogan contact data set 2021-03-16T16:39:24Z potentially infectious contact data set infectious disease control strategy census a census of infectious disease control strategies put into place to reduce infection acquisitions that are part of an infection in an ecosystem. William R. Hogan 2021-03-16T16:43:04Z control strategy census school closure infectious disease control strategy census an infectious disease control strategy census that is about school closure infectious disease control strategies implemented in a particular geographical region. William R. Hogan 2021-03-16T16:44:03Z This class represents datasets about strategies for school closure. Datasets about individual actual school closures go elsewhere. school closure control strategy census vaccination infectious disease control strategy census William R. Hogan 2021-03-16T16:47:09Z This class is an inventory of vaccination control strategies, not vaccinations themselves. So it should be a list of things like "Publix vaccination plan", "Alachua county vaccination plan", "Sam's Club vaccination plan", etc. And not a list of individual vaccinations given to actual patients (see population vaccination census) vaccination control strategy census population vaccination census vaccine / immunization registry data, vaccination / immunization records extracted from an EHR a population treatment census that is about one or more vaccinations of organisms in a population. William R. Hogan vaccination census 2021-03-16T16:48:42Z vaccination administration census dataset about excess mortality in a population A population mortality dataset that compares deaths in the population during one time interval to deaths in the population during a previous time interval and reports an estimate of how many more or less deaths occurred in the later time interval. William R. Hogan Often used during epidemics or pandemics to estimate the death toll. excess mortality dataset census of supplies of vaccine products A control strategy inventory census that counts available vaccine doses of one or more similar vaccines. William R. Hogan vaccine availability https://orcid.org/0000-0002-9881-1017 2022-02-01T00:03:00Z Motivated my MIDAS coordination center indexing of COVID-19 data, software, etc. By "similar vaccines" we typically mean same pathogen, but could be similar in other ways (requiring refrigeration of a certain kind). census of vaccination supplies census of facilities that conduct clinical laboratory tests A census of facilities that conduct clinical laboratory testing. William R. Hogan testing availability https://orcid.org/0000-0002-9881-1017 2022-02-01T00:10:00Z The census might also include information about each facility such as operating hours, address, accessibility, and so on. laboratory testing facility census model for disease transmission parameter estimation An algoirthm that is used to estimate the "true" values of certain parameters of disease transmission and/or forecasting. William R. Hogan 2022-09-18T17:51:00 Examples of parameters estimated include R0, transmissibility, infectious period. parameter estimation model An algorithm that operates on a representation of some portion of reality and that representation has a structure with nodes that stand for certain entities and edges that state some direct or indirect relationship between pairs of entities. William R. Hogan 2022-09-18T18:00:00 The algorithm might involve also generating or creating the network structure in addition to operating on it. network model laboratory testing capacity action specification An action specification giving the number of laboratory tests of a certain type that it is possible to perform in a given population during a specific time interval. William R. Hogan 2022-09-18T18:21 laboratory testing capacity data set about Earth's atmospheric weather A data set about the Earth's atmospheric weather William R. Hogan 2022-09-18T18:34:00 weather data set monkeypox disease inhering in a human being A monkeypox disease inhering in a human being. William R. Hogan 2022-09-18T18:51:00 requested by MIDAS CC human monkeypox A disease surveillance that detects evidence of the presence of pathogens in sewage. Matthew Diller sewage disease surveillance William R. Hogan See the CDC's explanation of wastewater surveillance, and how it uses the term 'wastewater' synonymously with 'sewage', here: https://www.cdc.gov/nwss/wastewater-surveillance.html. wastewater disease surveillance A count of simulated or physical individuals in a population. Matthew Diller population count A disease surveillance data set that is about some wastewater disease surveillance. Matthew Diller sewage surveillance data William R. Hogan wastewater surveillance data set A scalar measurement datum that is about some population and is normalized by unit land area in a particular geographical region. Matthew Diller William R. Hogan population density datum An individual treatment control strategy in which individuals maintain a certain distance from other individuals during a social act. Matthew Diller William R. Hogan physical distancing infectious disease control measure A place closure control strategy in which only selected places in a geographical region are permitted to stay open and travel is permitted only for people employed by certain organizations. Matthew Diller William R. Hogan The places that are allowed to stay open are typically selected by the local or state government, and often include hospitals, many healthcare facilities, food stores and food banks, and law enforcement and emergency services. lockdown infectious disease control measure A count of cases in an epidemic that is about the entire temporal interval occupied by the epidemic. William R. Hogan A count of cases from the beginning of the epidemic until recently. The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin. cumulative epidemic case count A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic. William R. Hogan A count of cases in an epidemic that spans a shorter interval, such as a particular day or a week. Incident case counts are measured according to regular intervals, typically day or week. The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin. incident epidemic case count A count of processes in which a population and/or its members participate during a given temporal region. William R. Hogan A count of certain type of event that occurs within a population, such as deaths, infections, births, and so on during a particular time. As the population is typically geographically defined (among other ways), the count is most often constrained to particular location in addition to a given time. count of events occurring in a population A count of death events that occurred in a population in a given temporal region. William R. Hogan population death count count of deaths in a population A count of vaccination events that occurred in a population during a temporal region. William R. Hogan population vaccination count A count of vaccinations in a population during a particular time. count of vaccinations in a population A count of hospital stays in a population during a temporal region. William R. Hogan population hospitalization count A count of hospitalizations in a population during a particular time. count of hospital stays in a population A count of infections (process) that occurred in a population in a given temporal region. William R. Hogan population infection count A count of infections in a population during a particular time. count of infections in a population A cumulative infection count where the infections are an occurrent part of the same epidemic, and the reference interval is the interval occupied by the entire epidemic. William R. Hogan cumulative epidemic infection count An incident infection count where the infections are an occurrent part of the same epidemic, and the temporal interval over which the count is made is a proper part of the reference interval. William R. Hogan incident epidemic infection count A cumulative death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic. William R. Hogan cumulative epidemic death count An incident death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval. William R. Hogan incident epidemic death count A cumulative hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic. William R. Hogan cumulative epidemic hospitalization count An incident hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval. William R. Hogan incident epidemic hospitalization count A cumulative vaccination count where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the reference interval is the temporal interval occupied by the entire epidemic. William R. Hogan cumulative epidemic vaccination count An incident vaccination count where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is a proper part of the reference interval. William R. Hogan incident epidemic vaccination count An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization. William R. Hogan An intent to be vaccinated in the future. intent to be vaccinated An intentionality directed at future participation in a vaccination as the administrator of a vaccine or other immunization to an organism with an immune system. William R. Hogan An intention to give a vaccine to someone or an animal. intent to vaccinate A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab. William R. Hogan vaccination with nirsevimab A count of vaccinations in a population that is the total number of a given type of vaccines administered during a reference temporal interval. William R. Hogan The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic or vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. cumulative vaccination count A count of vaccinations in a population that is the number of a given type of vaccines administered during a proper occurrent part of a reference temporal interval. William R. Hogan The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. incident vaccination count A count of infections in a population that is the total number of infections that occur during a reference temporal interval. William R. Hogan The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. cumulative infection count A count of infections in a population that is the number of infections of a given type that occurred during a proper occurrent part of a reference temporal interval. William R. Hogan The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. incident infection count A count of hospital stays in a population that is the total number of hospitalizations that occur during a reference temporal interval. William R. Hogan The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. cumulative hospitalization count A count of hospital stays in a population that is the number of hospital stays that occurred during a proper part of a reference temporal interval. William R. Hogan The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. incident hospitalization count A count of deaths in a population that is the total number of deaths that occur during a reference temporal interval. William R. Hogan The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. cumulative death count A count of deaths in a population that is the number of deaths that occurred during a proper part of a reference temporal interval. William R. Hogan The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. incident death count A count of disease cases that is the total number of individuals who come to meet the criteria of some case definition during a reference temporal interval. William R. Hogan The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. cumulative case count A count of cases in a population that is the number of individuals who come to meet the criteria of some case definition during a proper part of a reference temporal interval. William R. Hogan The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. incident case count guardian's intent to have a ward under their care vaccinated An intentionality inhering in a person bearing a guardian role and that is directed at their future participation in an authorization for the vaccination or other immunization of a person under their care and who bears a ward role. William R. Hogan The intent of a guardian to have a ward under their care vaccinated in the near future. Legally, this covers the situation of a parent intending to have their child vaccinated. That is because the parent(s) is(are) the natural gaurdian of the child. Other individuals appointed by a court as guardian are legal guardians. If the specific case of parent / child is required, we could create a subclass of this one where the guardian = parent of the ward, and ward = child. However, that could get into issues of adoption, etc. At the current time we do not have guardian role and ward role classes in OMRSE. intent to have a ward vaccinated organism reproduction The process by which new organisms are created from existing ones. William R. Hogan Reproduction reproduction An intent to have a ward vaccinated where the guardian is a parent (natural or adoptive) and the ward is a child (natural or adopted) of that parent, and the parent has not otherwise been legally barred from making healthcare decisions for the child. William R. Hogan Intent to have one's child vaccinated. The case of adult children is eliminated through the use of guardian and ward roles in the definition. The parent no longer has a guardian role, and the child no longer has a ward role, once the child is of legal age to make their own decisions. That is, those roles cease to exist. intent to have a child vaccinated epidemic simulator action specification William R. Hogan epidemic simulator action specification infectious disease control strategy action specification William R. Hogan infectious disease control strategy action specification individual treatment control strategy action specification William R. Hogan individual treatment control strategy action specification creating a data set A planned process that has a data set as its specified output. William R. Hogan data set creation dataset creation dataset creating creating a copyright license A planned process that has a copyright license as its specified output. William R. Hogan copyright license creation Note: for less than 24 hours, this class was a bit more specific to software licenses, but it did not have the equivalent class axiom during that time. creating a copyright license copyright license for a creative work A document that is about the legal rights, claims, and obligations of a legal person (person or organization) under copyright law, and how that legal person intends for those rights, claims, and obligations to be handled/managed by users of the creative work to which this document is attached. William R. Hogan Can be for any creative work including fiction. But the license itself is an ICE, and refers to real claims and obligations. copyright license data service software application A software application that implements a data service. William R. Hogan data service software TODO facultative role A role borne by an organism in virtue of the fact that it is in intimate association with one or more organisms of different species, and is realized by bodily benefit to that organism as an occurrent part of a symbiosis with the other organisms. This bodily benefit takes the place of the organism or some relatively isolated part of the organism realizing some normal homeostasis disposition itself. facultative role 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 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] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. 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] An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. 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 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 A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) 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 (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (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] A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. characteristic specifically dependent continuant https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) 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 (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (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 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 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] Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries. Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital Synonyms: substance aggregate object aggregate 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] 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. 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] Interval 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 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. 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]) The usage or intended usage of a drug product to act against a viral infection of a host. antiviral drug A viral infectious disease that has_material_basis in Zika virus, which is transmitted_by Aedes aegypti mosquitoes and targets neural progenitor cells and neuronal cells in all stages of maturity and has_symptom fever, has_symptom rash, has_symptom headaches and has_symptom joint pain. http://purl.obolibrary.org/obo/doid.owl ICD10:U06 ICD10CM:A92.8 MESH:D000071243 Zika virus disease Zika fever A viral infectious disease that results_in infection, has_material_basis_in Dengue virus [NCBITaxon:12637] with four serotypes (Dengue virus 1, 2, 3 and 4), which are transmitted_by Aedes mosquito bite. The infection has_symptom fever, has_symptom severe headache, has_symptom severe pain behind the eyes, has_symptom joint pain, has_symptom muscle and bone pain, has_symptom rash, and has_symptom mild bleeding. http://purl.obolibrary.org/obo/doid.owl DOID:0050142 ICD10CM:A90 ICD9CM:061 MESH:D003715 NCI:C34528 SNOMEDCT_US_2016_03_01:154345006 SNOMEDCT_US_2016_03_01:266194002 SNOMEDCT_US_2016_03_01:38362002 UMLS_CUI:C0011311 Dengue Fever breakbone fever classic dengue disease_ontology classical dengue DOID:12205 dengue disease A dengue disease that occurs when a person experiences a second infection with a heterologous Dengue virus serotype, which is transmitted_by Aedes mosquito bite. The infection has_symptom hemorrhagic lesions of the skin, has_symptom thrombocytopenia, has_symptom reduction in the fluid part of the blood, and has_symptom high fever. http://purl.obolibrary.org/obo/doid.owl ICD10CM:A91 MESH:D019595 NCI:C34683 SNOMEDCT_US_2016_03_01:186598001 SNOMEDCT_US_2016_03_01:186599009 SNOMEDCT_US_2016_03_01:20927009 UMLS_CUI:C0019100 DHF disease_ontology Dengue haemorrhagic fever DOID:12206 dengue hemorrhagic fever A viral infectious disease that results in infection of primates, rodents and humans, located in skin, has_material_basis_in Monkeypox virus, which is transmitted by contact with the animal's blood, body fluids, rash, or with the body fluids of a sick person, transmitted by fomites, and transmitted by respiratory droplets. The infection has symptom fever, has symptom muscle ache, has symptom headache, and has symptom lymphadenopathy. http://purl.obolibrary.org/obo/doid/releases/2022-08-29/doid.owl GARD:10722 ICD10CM:B04 ICD9CM:059.01 MESH:D045908 NCI:C128421 SNOMEDCT_US_2021_09_01:240466002 UMLS_CUI:C0276180 url:http://www.cdc.gov/ncidod/monkeypox/factsheet2.htm disease_ontology DOID:3292 monkeypox A viral infectious disease that results_in infection, located_in respiratory tract, has_material_basis_in Influenzavirus A, has_material_basis_in Influenzavirus B, or has_material_basis_in Influenzavirus C, which are transmitted_by droplet spread of oronasal secretions during coughing, sneezing, or talking from an infected person. It is a highly contagious disease that affects birds and mammals and has_symptom chills, has_symptom fever, has_symptom sore throat, has_symptom runny nose, has_symptom muscle pains, has_symptom severe headache, has_symptom cough, and has_symptom weakness. http://purl.obolibrary.org/obo/doid.owl DOID:8468 ICD10CM:J11.1 ICD9CM:487 MESH:D007251 NCI:C53482 SNOMEDCT_US_2016_03_01:155559006 SNOMEDCT_US_2016_03_01:155562009 SNOMEDCT_US_2016_03_01:195931008 SNOMEDCT_US_2016_03_01:266353003 SNOMEDCT_US_2016_03_01:266393000 SNOMEDCT_US_2016_03_01:6142004 UMLS_CUI:C0021400 Influenza with non-respiratory manifestation (disorder) Influenza with other manifestations Influenza with other manifestations (disorder) Influenza with other manifestations NOS (disorder) flu influenza with non-respiratory manifestation disease_ontology DOID:8469 influenza a material entity (1) containing at least one scattered molecular aggregate as part (the active ingredient) and (2) that is the bearer of a clinical drug role William Hogan http://purl.obolibrary.org/obo/dron.owl William Hogan drug product A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. http://purl.obolibrary.org/obo/envo.owl portion of environmental material ENVO ENVO:00010483 Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. environmental material An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system. http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl ORCID:0000-0002-4366-3088 2013-04-07T14:35:18Z DOI:10.1186/2041-1480-4-43 envoPolar A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional. environmental condition Water vapour is a vapour which is the gas phase of water. http://purl.obolibrary.org/obo/envo.owl ORCID:0000-0002-4366-3088 2013-10-10T07:58:18Z aqueous vapor aqueous vapour water vapor ENVO ENVO:01000266 Perhaps a better relation between water vapour and water can be found in or added to RO? water vapour Atmospheric water vapour is water vapour that is part of an atmosphere. http://purl.obolibrary.org/obo/envo.owl ORCID:0000-0002-4366-3088 2013-10-10T08:22:07Z atmospheric water vapor ENVO ENVO:01000268 atmospheric water vapour Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity. http://purl.obolibrary.org/obo/envo.owl precipitation "process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet) hydrological precipitation process A temperature that inheres in some portion of air. Draft class. In discussion in Issue #278. http://purl.obolibrary.org/obo/envo.owl air temperature A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely. This class is to be populated by inference. http://purl.obolibrary.org/obo/envo.owl gas gaseous environmental material Environmental variability which inheres in an astronomical body part or in outer space. http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl https://en.wikipedia.org/wiki/Space_weather https://en.wikipedia.org/wiki/Weather This class refers to all weather, including atmospheric and space weather. Please use a subclass for more specificity. weather Weather which inheres in an atmosphere. http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl https://en.wikipedia.org/wiki/Weather This class refers to the common usage of "weather", referencing the state of a (part of) an astronomical body's atmosphere. atmospheric weather A condition which inheres in an environmental system by virtue of that system undergoing variation in its composition, the distribution of the qualities its components bear, and/or in the processes which occur within it and which it participates in. http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl This class is very general, but the nature of environmental variability is indeed quite variable. This class may be refined once we have more subclasses to consider. environmental variability http://purl.obolibrary.org/obo/envo.owl Should environmental feature become something more towards a disposition, the assert would be updated to something like "has participant (environmental system or (material entity and has disposition some environmental feature))". There are several issues surrounding the reconcilliation of environmental feature and environmental system, both theoretical and practical. environmental system process The temperature of a environmental material. http://purl.obolibrary.org/obo/envo.owl environmental material temperature temperature of environmental material The temperature of a air. http://purl.obolibrary.org/obo/envo.owl air temperature temperature of air A molecular assay that is used to analyze metagenomic data; genetic material recovered directly from environmental samples for genomic research. PERSON: Nicole Vasilevsky community genomic analysis ecogenomic analysis environmental genomic analysis http://en.wikipedia.org/wiki/Metagenomics http://purl.obolibrary.org/obo/ero.owl metagenomics analysis A set of related web pages containing content such as text, images, video, audio, etc., prepared and maintained as a collection of information on a particular subject. http://purl.obolibrary.org/obo/fbcv.owl pub_type FBcv:0000667 website A publication issued on a regular, ongoing basis containing separate research articles and other writings such as reviews, comments and conference reports. http://purl.obolibrary.org/obo/fbcv.owl djs93 2012-07-10T04:08:06Z MeSH:D020492 pub_type Periodicals FBcv:0000787 journal An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii) William R. Hogan In some cases, geopolitical entities possess uninhabited geographical regions. However, it is that case that it controls the movement of people in and out of those regions, and its laws apply to those regions. geopolitical entity true obsolete aggregate of governmental organizations An aggregate of geopoliticial entities. Examples include the group of states of the United States, the nations of North America, and so on. William R. Hogan taken over by GEO_0000000401 obsolete group of governmental organizations true A geopolitical entity that is self contained and recognizes no higher political authority than itself. William R. Hogan nation true a governmental organization that has a local, regional, or territorial government that recognizes a sovereign state as its higher political authority Amanda Hicks William R. Hogan subnational entity A subnational entity that is the primary organizational member of a nation, is subject to the full set of laws of the nation, enjoys all the privileges established under the laws of the nation, is not a member of any other geopolitical entity, and itself governs a part of the geographical region governed by the nation. Amanda Hicks William R. Hogan administrativeLocations examples: Northern Ireland, Florida major administrative subdivision A subnational entity that does not possess full political independence or sovereignty as a sovereign state, but remains politically outside of the controlling state and controls a geographical region that is outside the controlling state's integral region. Amanda Hicks William R. Hogan Typically, the common feature is that the dependency does not conduct foreign affairs, and relegates this authority to the sovereign state. But otherwise, it is largely or completely autonomous relative to the administrative subdivisions. Examples include Puerto Rico (U.S.), Guam (U.S.), Greenland (Denmark), French Polynesia (France), and Falkland Islands (United Kingdom). geopolitical dependency 2 An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common. Amanda Hicks Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc. aggregate of major administrative subdivisions group of major administrative subdivisions 2 An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common. Amanda Hicks Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies. aggregate of dependencies group of dependencies subcontinental land mass contiguous continental land mass per the definition of 'contiguous' of "being in actual contact : touching along a boundary or at a point", these land masses share boundaries with other land masses that are part of the same continent, and thus are not surrounded by water like an island. At some point, we need an 'adjacent to' relation if BFO doesn't provide it. One question is whether this class encompasses fiat parts of islands. contiguous land mass 2 An aggregate of organizations that is not itself a governmental organization, has only governmental organizations as members, and has at least two governmental organizations as members. William R. Hogan aggregate of governmental organizations A subcontinental land mass that is part of an island and includes part of the land surface of the island. William R. Hogan It cannot be a part of the island, for example, that is below water. contiguous island land mass aggregate of contiguous land masses geographical entity of astronomical body A material entity that is (1) a bona fide or fiat object part of the crust, any bodies of liquid on or contained within the crust, or planetary boundary layer (if present) of a terrestrial planet (including Earth), dwarf planet, exoplanet, natural satellite, planetesimal, or small Solar System body, and that (2) overlaps the planetary surface (including having a boundary that coincides with part of the planetary surface). Mathias Brochhausen Matt Diller William R. Hogan Includes atmosphere, crust, geographical regions (e.g., the geographical region over which the state of Florida has jurisdiction), bodies of water, mountains, etc. Generally, an individual organism is a distinct object that is not a part of the Earth, although this requires more thought. But the intent is definitely for this class to NOT subsume organism universally. Human beings are contained within, but not part of, the Earth, for example. Note that despite the word 'planetary' in 'planetary surface', it refers generally to surface of dwarf planets, asteroids, moons, etc. We note that not all planets have a surface per se (e.g., gas giants such as Jupiter and Saturn). So only planets, natural satellites, etc. with a planetary surface (with or without a planetary boundary layer) have geographical entities. We note that the term 'geography' is also applied to the Earth's moon, Mars, Venus, and possibly even other moons and planets in our own solar system and beyond. Thus, we are attempting to define things generally enough that they could be reused for the geographical entities/features on the Moon, Mars, other planets, exoplanets, other natural satellites (a.k.a moons), asteroids, etc. geographical entity A geographical entity that has at least one bona fide boundary. geographical feature A geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface. A site designated by some relative spatial orientation. François Modave Mathias Brochhausen Matt Diller Matthew Diller William R. Hogan William R. Hogan An arbitrary part of the Earth defined by human-made boundaries and/or natural features such as rivers. Location geographical region body of water continent land mass island An object aggregate of geographical entities aggregate of geographical entities aggregate of geographical features aggregate of islands geopolitical organization Amanda Hicks geopoli organization Amanda Hicks "Although the very meaning of the term is controversial, it involves authoritative decsionmaking in areas that once were part of national legal frameworks, the government, the sovereign state, or the public sector." Karns and Mingst (2004) p. 14. Katrina Donovan Examples: private bond-rating agencies such as Moody's Investors Service, International Chamber of Commerce, Worldwide Responsible Apparel Manufacturing Principles, Forest Stewardship private governance organization a geopolitical organization that is voluntary and private, whose members are individual persons or organizations that come together to acheive a common purpose. NGOs are private voluntary organizations whose members are individuals or associations that come together to acheive a common purpose. Some organizations are formed to advocate a particular cause such as human rights, peace, or envirnomental projetion. Others are established to provide services such as disaster relief, humantarian aid in war-torn socieities, or development assistance. ... National level groups are often called interest or pressure groups, and many of them are now linked to counterpart groups in other countries through transnational networks or federations. International NGOs, like IGOs, may draw their members from one region or several regions, and they may have very specific functions or be multi-functional. Karns and Mingst (2004) p. 10f. Katrina Donovan Examples: Internaltion Federation of Red Cross and Red Crescent Societies, Oxfam, CARE, Doctors Without Borders, World Wildlife Fund, Transparency International, Human Rights Watch, Amnesty International, and Save the Children. nongovernmental organization an intergovernmental organization that has at least three member states, that has activies in at least three states, and that is unified by some formal intergovernmental agreement Amanda Hicks "IGOs are organizations whose memebers include at lesat three states, that have activities in several states, and whose members are held together by a formal intergovernmental agreement ... These organizations range in size from three members (North American Free Trade Argreement [NAFTA]) to more than 190 memembers (Universal Postal Union (UPU)]. Memebers may come from primarily one georgraphic regioni (Oragnaization of American States [OAS]) or from all geographic regions (World Bank). although soem IGOs are designed to achieve a single purpose (Organization of Petroleum exporting countries [OPEC]), others have been developed for multiple tasks (United Nations [UN}). ... IGOs are recognized subjects of international law with separate standing fromt heir member states." Karns and Mingst I(2004) p. 7 Katrina Donovan examples: North American Free Trade Argreement [NAFTA] , Universal Postal Union [UPU], Oragnaization of American States [OAS], World Bank), Organization of Petroleum exporting countries [OPEC] United Nations [UN[, The World Trade Organization [WTO], The World Health Organization [WHO], UNICEF intergovernmental organization A governmental organization with a defined territory on which it exercises internal and external sovereignty, a permanent population, a government, and the capacity to enter into relations with other sovereign states. William R. Hogan de facto sovereign state de facto state nation nation state http://en.wikipedia.org/wiki/Sovereign_state Per Wikipedia, the word 'nation' does not always refer to soverign states. For example, the "nation of Islam". sovereign state An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii). Note: this definition was taken over from "geopolitical organization". Amanda Hicks IMPORTANT: The label "geopolitical organization" was previously used for OMRSE_00000044 (governmental organization). "geopoli organization" is a label for a new and different class. governmental organization 2 An object aggregate that is not itself a geopolitical organization and whose members are only geopolitical organizations that have some feature in common Amanda Hicks William R. Hogan http://purl.obolibrary.org/obo/omrse.owl aggregate of geopolitical organizations An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common. Amanda Hicks http://purl.obolibrary.org/obo/omrse.owl Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies. obsolete aggregate of dependencies true An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common Amanda Hicks http://purl.obolibrary.org/obo/omrse.owl Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc. obsolete aggregate of major administrative subdivisions true 2 An aggregate of governmental organizations that is not itself a sovereign state and whose members are only sovereign states that have some feature in common William R. Hogan http://purl.obolibrary.org/obo/omrse.owl examples: all the sovereign states in North America, all the sovereign states with a GDP below or exceeding a particular quantity of money, all the sovereign states with a constitutional monarchy, all the sovereign states who belong to the U.N. (which is different than the U.N. itself), etc. aggregate of sovereign states geodetic coordinate measurement datum A measurement of location on the Earth that uses a single number to specify a coordinate in a coordinate system known as a geodetic datum. Josh Hanna William R. Hogan latitude and longitude are key subtypes geodetic coordinate measurement datum geodetic datum A coordinate system, and a set of reference points, used to locate places on the Earth (or similar objects). Josh Hanna William R. Hogan Wikipedia: https://en.wikipedia.org/wiki/Geodetic_datum Date accessed: 2015-04-13 Every latitude and longitude measurement is with respect to a geodetic datum. Most common ones in use are NAD83 and WGS84. geodetic datum planar angular measurement unit label plane angle measurement unit label A sovereign state whose political sovereignty has been recognized by the United Nations, in accordance with international law. Matthew Diller de jure state Sovereignty, in the legal sense, is acquired by a state upon receiving recognition by the international community. However, without specifying that this recognition can only be acquired through full membership to the United Nations, a non-arbitrary standard would be difficult, if not impossible, to come by since there are a good many sovereign states whose sovereignty is not explicitly recognized by one or more states. Given that the de facto criteria for sovereignty must be achieved prior to membership to the UN General Assembly and that every member therein is considered to be "international recognized," full membership to the UN is a sufficient criterion for de jure sovereignty. This can be further justified by noting that, in cases where UN member X claims to not recognize the sovereign status of UN member Y, the diplomatic and political behavior of member X towards Y nevertheless tacitly implies that it recognizes Y's sovereignty. de jure sovereign state A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. molecular function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. This is the same as GO molecular function gene product or complex activity molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. GOC:pdt Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. immune response The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. jl 2012-09-20T14:06:08Z GO:0023032 GO:0044708 GO:0044709 Wikipedia:Behavior behavioral response to stimulus behaviour behavioural response to stimulus biological_process single-organism behavior GO:0007610 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). behavior The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. GOC:ems GOC:jl ISBN:0395448956 PMID:20160973 A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. https://github.com/geneontology/go-ontology/issues/24968 jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 A biological process is an evolved process Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological process biological_process A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle. GO:0022415 Wikipedia:Viral_life_cycle virus process biological_process viral infection virulence GO:0016032 See also the biological process terms 'viral infectious cycle ; GO:0019058' and 'lysogeny ; GO:0030069'. viral process A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle. GOC:bf GOC:jl GOC:mah virus process GOC:bf GOC:jl true Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. Reactome:R-HSA-6788855 Reactome:R-HSA-6788867 phosphokinase activity GO:0016301 Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. kinase activity Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. ISBN:0198506732 Reactome:R-HSA-6788855 FN3KRP phosphorylates PsiAm, RibAm Reactome:R-HSA-6788867 FN3K phosphorylates ketosamines A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome. GO:0019067 viral assembly, maturation, egress, and release biological_process lytic viral life cycle viral infectious cycle viral replication GO:0019058 viral life cycle A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome. ISBN:1555811272 viral assembly, maturation, egress, and release GOC:bf GOC:jl viral infectious cycle GOC:bf GOC:jl viral replication GOC:bf GOC:jl The specific behavior of an organism that is associated with reproduction. https://github.com/geneontology/go-ontology/issues/23491 jl 2012-09-19T16:01:37Z GO:0033057 GO:0044704 GO:0044705 reproductive behavior in a multicellular organism reproductive behaviour multi-organism reproductive behavior multicellular organism reproductive behavior biological_process single-organism reproductive behavior GO:0019098 reproductive behavior The specific behavior of an organism that is associated with reproduction. GOC:jl GOC:pr A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid). https://github.com/geneontology/go-ontology/issues/22929 Wikipedia:Sexual_reproduction biological_process GO:0019953 Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times. sexual reproduction A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid). Wikipedia:Sexual_reproduction A type of reproduction in which new individuals are produced from a single organism, either from an unfertilized egg or from a single cell or group of cells. https://github.com/geneontology/go-ontology/issues/22929 Wikipedia:Asexual_reproduction biological_process parthenogenesis GO:0019954 asexual reproduction A type of reproduction in which new individuals are produced from a single organism, either from an unfertilized egg or from a single cell or group of cells. ISBN:0387520546 PMID:22977071 PMID:28779329 PMID:29559496 parthenogenesis Wikipedia:Parthenogenesis A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. https://github.com/geneontology/go-ontology/issues/27054 jl 2012-09-19T15:56:06Z GO:0044702 Wikipedia:Reproduction biological_process single organism reproductive process GO:0022414 reproductive process A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GOC:dph GOC:isa_complete Any biological process, occurring at the level of a multicellular organism, pertinent to its function. https://github.com/geneontology/go-ontology/issues/27189 jl 2012-09-19T16:07:47Z GO:0044707 GO:0050874 organismal physiological process biological_process single-multicellular organism process GO:0032501 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. multicellular organismal process Any biological process, occurring at the level of a multicellular organism, pertinent to its function. GOC:curators GOC:dph GOC:isa_complete GOC:tb OBSOLETE. The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. https://github.com/geneontology/go-ontology/issues/27054 GO:0048609 biological_process GO:0032504 The reason for obsoletion is that this term is equivalent to multicellular organismal reproductive process. obsolete multicellular organism reproduction true OBSOLETE. The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GOC:isa_complete GOC:jid A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts. https://github.com/geneontology/go-ontology/issues/14807 https://github.com/geneontology/go-ontology/issues/20191 GO:0043298 GO:0044404 GO:0072519 GO:0085031 commensalism host-pathogen interaction parasitism biological_process symbiosis symbiosis, encompassing mutualism through parasitism symbiotic interaction symbiotic interaction between host and organism symbiotic interaction between organisms symbiotic interaction between species symbiotic process GO:0044403 biological process involved in symbiotic interaction A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts. GOC:cc PMID:31257129 Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction. Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. https://github.com/geneontology/go-ontology/issues/18563 GO:0030260 GO:0044411 GO:0051806 GO:0051828 GO:0051830 GO:0075052 GO:0085027 GO:0085028 entry into host host invasion host penetration invasion into host invasion of host penetration into host entry into cell of other organism during symbiotic interaction entry into host cell via penetration peg entry into host via a specialized structure during symbiotic interaction entry into host via enzymatic degradation of host anatomical structure entry into host via enzymatic degradation of host cuticle penetration into host via a specialized structure penetration into host via a specialized structure during symbiotic interaction biological_process entry into cell of other organism involved in symbiotic interaction entry into host through host barriers entry into other organism during symbiotic interaction entry into other organism involved in symbiotic interaction invasion into other organism invasion of other organism invasive growth other organism invasion GO:0044409 entry into host symbiont entry into host Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction. GOC:vw host penetration GOC:vw penetration into host GOC:vw entry into cell of other organism during symbiotic interaction GOC:tb penetration into host via a specialized structure GOC:vw penetration into host via a specialized structure during symbiotic interaction GOC:vw entry into other organism during symbiotic interaction GOC:tb Any process evolved to enable an interaction with an organism of a different species. https://github.com/geneontology/go-ontology/issues/20191 interaction with another species interspecies interaction interspecies interaction between organisms interspecies interaction with other organisms biological_process GO:0044419 biological process involved in interspecies interaction between organisms Any process evolved to enable an interaction with an organism of a different species. GOC:cc The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. https://github.com/geneontology/go-ontology/issues/27054 organismal reproductive process reproductive process in a multicellular organism biological_process GO:0048609 multicellular organismal reproductive process The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. GOC:dph GOC:jid GOC:tb Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. Gene Ontology: http://purl.obolibrary.org/obo/go.owl establishment of localization An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism. https://github.com/geneontology/go-ontology/issues/20191 GO:0044112 GO:0044116 GO:0044117 GO:0044119 GO:0044121 GO:0044123 GO:0044125 interaction with host growth of symbiont in host growth of symbiont in host cell growth of symbiont in host organelle growth of symbiont in host vacuole biological_process GO:0051701 biological process involved in interaction with host An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism. GOC:cc A biological process which involves another organism of the same or different species. multi-organism process conditional specification A directive information entity that specifies what should happen if the trigger condition is fulfilled. PlanAndPlannedProcess Branch OBI branch derived OBI_0000349 conditional specification measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A data item label that denotes a unit of measure. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done 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. PERSON: Alan Ruttenberg PERSON: Melanie Courtot http://purl.obolibrary.org/obo/obi.owl measurement unit label 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 narrative object Examples of narrative objects are reports, journal articles, and patents submission. A narrative object is an information content entity that is a set of propositions. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions person:Chris Stoeckert OBI_0000013 group:OBI narrative object 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 obsolete_artifact true data item label datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label An information content entity that is part of some data item and is used to partially define the denotation of that data item. http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO datum label 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. http://purl.obolibrary.org/obo/obi.owl data item label datum label software Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI software obsolete_digital entity A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality' person:Chris Stoeckert OBI_0000261 group:OBI obsolete2_digital entity true journal article Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. A report that is published in a journal. PERSON: Alan Ruttenberg PERSON: Chris Stoeckert OBI_0000159 group:OBI journal article information carrier In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. A quality of an information bearer that imparts the information content 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. PERSON: Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy information carrier model number A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers Person: Alan Ruttenberg model number obsolete_material_entity true binary digital entity MS Word document, ZIP file, DICOM file, JPEG file A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity' digital_entity person:Chris Stoeckert OBI_0000244 group:OBI obsolete2_binary digital entity true The length of a ruler. a unit of measure is the quality of some material entity compared to which another quality is some multiple of. Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy obsolete_unit of measure true programming language R, Perl, Java A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. person:Alan Ruttenberg person:Chris Stoeckert OBI_0000058 group:OBI programming language data item Data items include counts of things, analyte concentrations, and statistical summaries. An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item symbol a serial number such as "12324X" a stop sign a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol numeral A symbol that denotes a number. PERSON: Jonathan Rees numeral information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity integer numeral A numeral that denotes an integer PERSON: Jonathan Rees integer numeral 1 1 scalar measurement datum 10 feet. 3 ml. A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot http://purl.obolibrary.org/obo/obi.owl scalar measurement datum 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 time trigger PlanAndPlannedProcess Branch time trigger obsolete_study interpretation A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application." 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. The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead. Lawrence Hunter PERSON: Alan Ruttenberg PERSON: Jennifer Fostel PERSON: Melanie Courtot conclusion OBI_0000005 obsolete_study interpretation true dot plot Dot plot of SSC-H and FSC-H. A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. person:Allyson Lister person:Chris Stoeckert OBI_0000123 group:OBI dot plot graph A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. PERSON: Lawrence Hunter person:Alan Ruttenberg person:Allyson Lister OBI_0000240 group:OBI graph text based digital entity XML file, C++ source code file A text based digital entity is a digital entity that is encoded so that it only contains text characters. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document' digital_entity person:Chris Stoeckert OBI_0000132 group:OBI obsolete2_text based digital entity true rule example to be added A rule is an executable which guides, defines, restricts actions. MSI PRS OBI_0500021 PRS rule contour plot Contour plot of SSC-H, FSC-H, and FL1-H. generically_dependent_continuants person:Allyson Lister person:Chris Stoeckert OBI_0000246 group:Flow Cytometry community contour plot report figure A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report Replaced by defined version of figure person:Alan Ruttenberg person:Allyson Lister OBI_0000027 group:OBI obsolete2_report figure true algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. Philippe Rocca-Serra PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm software interpreter R program, Perl interpreter, Java virtual machine A software interpreter is a software application that executes some specified input software. Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter person:Alan Ruttenberg person:Chris Stoeckert OBI_0000199 group:OBI software interpreter 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 density plot Density plot of SSC-H and FSC-H. A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. person:Allyson Lister person:Chris Stoeckert OBI_0000179 group:Flow Cytometry community density plot 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: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI OBI_0000099 report report element A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page). 2009-03-16: needs some more work (clarify relations). 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements. 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 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion Replaced by textual entity and figure There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text PERSON: Alan Ruttenberg PERSON: Allyson Lister PERSON: Melanie Courtot GROUP:OBI OBI_0000001 obsolete_report element true binary executable Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007) 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity' person:Jennifer Fostel OBI_0000222 group:OBI obsolete2_binary executable true source code module The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. A source code module is a directive information entity that specifies, using a programming language, some algorithm. person:Alan Ruttenberg person:Chris Stoeckert OBI_0000039 group:OBI source code module report table A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion person:Alan Ruttenberg person:Allyson Lister OBI_0000265 group:OBI obsolete_report table true data format specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" PERSON: Alan Ruttenberg PlanAndPlannedProcess Branch OBI branch derived OBI_0000187 data format specification data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set image An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. person:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI image data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg 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, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg Clint Dowland OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 digital document A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity' person:Jennifer Fostel OBI_0000195 group:OBI obsolete2_digital document true measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI http://purl.obolibrary.org/obo/obi.owl measurement datum _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final. obsolete_identifier true version number A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version GROUP: IAO version number serial number A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-) GROUP: IAO serial number lot number A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. GROUP: IAO batch number lot number A settings datum is a datum that denotes some configuration of an instrument. 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable. Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. setting datum 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Need to rework digital entity. Digital quality was suggested by Barry. obsolete_digital quality true conclusion textual entity that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/23 Alan Ruttenberg: We need to work on the definition still Person:Alan Ruttenberg conclusion textual entity material information bearer A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. a brain a hard drive A material entity in which a concretization of an information content entity inheres. GROUP: IAO material information bearer histogram A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI histogram heatmap A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI heatmap Venn diagram A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Venn_diagram Venn diagram obsolete_survival curve A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://www.graphpad.com/www/book/survive.htm obsolete_survival curve true dendrogram Dendrograms are often used in computational biology to illustrate the clustering of genes. A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Dendrogram dendrogram scatter plot Comparison of gene expression values in two samples can be displayed in a scatter plot A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot scattergraph WEB: http://en.wikipedia.org/wiki/Scatterplot scatter plot A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. PERSON:Alan Ruttenberg PERSON:Joanne Luciano PERSON:Melanie Courtot WEB: http://en.wiktionary.org/wiki/photograph photograph photographic print A photographic print is a material entity upon which a photograph generically depends. PERSON:Alan Ruttenberg PERSON:Melanie Courtot photographic print obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification 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 citation Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183. A textual entity intended to identify a particular publication. PERSON: Lawrence Hunter citation author identification L. Hunter A textual entity intended to identify a particular author PERSON: Lawrence Hunter author identification institutional identification University of Colorado Denver School of Medicine A textual entity intended to identify a particular institution PERSON: Lawrence Hunter institutional identification caption Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool. A textual entity that describes a figure PERSON: Lawrence Hunter caption document title Textual characteristics of traditional and Open Access scientific journals are similar A textual entity that names a document PERSON: Lawrence Hunter document title table | T F --+----- T | T F F | F F A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions PERSON: Lawrence Hunter table table of abbreviations IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology A table where the constituent texts are abbreviations and their expansions PERSON: Lawrence Hunter table of abbreviations figure Any picture, diagram or table An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. PERSON: Lawrence Hunter figure diagram A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. A figure that expresses one or more propositions PERSON: Lawrence Hunter diagram 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 publication journal article, newspaper story, book, etc. A document that is the output of a publishing process. PERSON: Chris Stoeckert PERSON: Jie Zheng PERSON: Lawrence Hunter published document Revisit the term in Octorber 2020. Improve the defintion. publication publication about an investigation Most scientific journal articles A publication that is about an investigation PERSON: Lawrence Hunter scientific publication publication about an investigation patent US Patent 6,449,603 A document that has been accepted by a patent authority PERSON: Lawrence Hunter patent document part An abstract, introduction, method or results section. An information content entity that is part of a document. PERSON: Lawrence Hunter document part abstract The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes. PERSON: Lawrence Hunter precis abstract introduction to a publication about an investigation Section labelled 'introduction' of a typical scientific journal article A part of a publication about an investigation that is about the objective specification (why the investigation is being done) PERSON: Lawrence Hunter background introduction overview introduction to a publication about an investigation methods section The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article. A part of a publication about an investigation that is about the study design of the investigation PERSON: Lawrence Hunter experimental experimental methods experimental procedures experimental section method methodology methods methods section results section The section labelled 'results' in a typical scientific journal article A part of a publication about an investigation that is about a study design execution PERSON: Lawrence Hunter results results section discussion section of a publication about an investigation A part of a publication about an investigation that is about the study interpretation of the investigation PERSON: Lawrence Hunter discussion discussion section discussions discussion section of a publication about an investigation references section The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography" A part of a document that has citations as parts PERSON: Lawrence Hunter literature cited reference reference list references references section author list Lawrence Hunter and Kevin Brettonel Cohen A part of a document that enumerates the authors of the document PERSON: Lawrence Hunter author list institution list The University of Colorado Denver School of Medicine and the University of Colorado Boulder. A part of a document that has parts that are institution identifications associated with the authors of the document PERSON: Lawrence Hunter institution list author contributions section LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript. A part of a publication that is about the specific contributions of each author PERSON: Lawrence Hunter author contributions authors' contribution authors' contributions authors' roles contributions by the authors contributorship author contributions section acknowledgements section The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript Part of a publication that is about the contributions of people or institutions other than the authors. PERSON: Lawrence Hunter acknowledgement acknowledgements acknowledgment acknowledgments acknowledgements section footnote The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text. A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document. PERSON: Lawrence Hunter endnote footnotes footnote supplementary material to a document A part of a document that is segregated from the rest of the document due to its size PERSON: Lawrence Hunter additional file additional files additional information appendix electronic supplementary material electronic supplementary materials supplemental data supplemental information supplemental material supplementary data supplementary files supplementary information supplementary material supplementary materials supporting information supplementary material to a document table of contents A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred). PERSON: Lawrence Hunter table of contents table of figures A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred). PERSON: Lawrence Hunter table of figures running title A shorter version of a document title PERSON: Lawrence Hunter running title copyright section This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License. A document part that describes legal restrictions on making or distributing copies of the document PERSON: Lawrence Hunter copyright section 1 A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 Alan Ruttenberg AR notes: We need to discuss whether it should include site. cartesian spatial coordinate datum http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 1 A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region Alan Ruttenberg one dimensional cartesian spatial coordinate datum 1 1 A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region Alan Ruttenberg two dimensional cartesian spatial coordinate datum 1 1 1 A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region Alan Ruttenberg three dimensional cartesian spatial coordinate datum A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg length measurement datum denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Alan Ruttenberg Barry Smith, Werner Ceusters Barry Smith, Werner Ceusters denotator type denotator type A scalar measurement datum that is the result of measurement of mass quality 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg mass measurement datum hypothesis textual entity that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 A textual entity that expresses an assertion that is intended to be tested. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg hypothesis textual entity A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg time measurement datum 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 author role A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. PERSON: Alan Ruttenberg PERSON: Melanie Courtot author role A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing Person:Alan Ruttenberg data item extraction from journal article A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free. Person: Jie Zheng https://en.wikipedia.org/wiki/Publishing VEuPathDB publishing process A document that is in preparation for submission to be published. PERSON: Jie Zheng EFO_0001795 in preparation VEuPathDB document in preparation for publication Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. A planned process in which a document is created or added to by including the specified input in it. 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape Bjoern Peters wikipedia http://en.wikipedia.org/wiki/Documenting documenting line graph A line graph is a type of graph created by connecting a series of data points together with a line. PERSON:Chris Stoeckert PERSON:Melanie Courtot line chart GROUP:OBI WEB: http://en.wikipedia.org/wiki/Line_chart line graph A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry. Person:Alan Ruttenberg Person:Bjoern Peters Person:Melanie Courtot assigning a CRID assigning a centrally registered identifier Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. A planned process in which a CRID registry associates an information content entity with a CRID symbol PERSON:Alan Ruttenberg associating information with a CRID in the CRID registry associating information with a centrally registered identifier in its registry a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID. MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now. obsolete_establishing a CRID registry true 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. A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol 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. 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 Original proposal from Bjoern, discussions at IAO calls centrally registered identifier PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles. A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. Justin Whorton PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls https://github.com/information-artifact-ontology/IAO/issues/237 centrally registered identifier registry Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot looking up a CRID looking up a centrally registered identifier time stamped measurement datum pmid:20604925 - time-lapse live cell microscopy A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. Alan Ruttenberg experimental time series time sampled measurement data set written name "Bill Clinton" "The Eiffel Tower" "United States of America" A textual entity that denotes a particular in reality. PERSON: Bill Hogan https://github.com/information-artifact-ontology/IAO/issues/114 The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. written name A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software method A software module is software composed of a collection of software methods. PERSON: Melanei Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software module A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software library A software application is software that can be directly executed by some processing unit. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software application A software script is software whose instructions can be executed using a software interpreter. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software script abbreviation textual entity From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect. A textual entity listing abbreviations and their expansions that are used in a document. PERSON: Bill Baumgartner abbreviation textual entity abbreviations section The section labelled 'abbreviations' in a typical scientific journal article. A part of a document where abbreviations and their long-forms used within the document are listed. PERSON: Bill Baumgartner abbreviation and acronyms abbreviation list abbreviations abbreviations and acronyms abbreviations list abbreviations used definitions for abbreviations list of abbreviations list of abbreviations used non-standard abbreviations nonstandard abbreviations nonstandard abbreviations and acronyms abbreviations section author information section The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/) A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. PERSON: Bill Baumgartner author information authors’ information biographies contributor information author information section author information textual entity From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD. A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. PERSON: Bill Baumgartner author information textual entity author summary section The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/) A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers. PERSON: Bill Baumgartner author summary summary synopsis Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines) author summary section author summary textual entity From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX. A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). PERSON: Bill Baumgartner Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). author summary textual entity availability section The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained. PERSON: Bill Baumgartner availability availability of data data archiving data availability data availability statement data sharing statement availability section availability textual entity From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): Project home page:http://krux.googlecode.com A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained. PERSON: Bill Baumgartner availability textual entity case report section The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/) A part of a document about the medical history of a specific patient as it relates to the topic of the document. PERSON: Bill Baumgartner case presentation case report case report section case report textual entity Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension. A textual entity that expresses a detailed account of a portion of the medical history for a specific patient. PERSON: Bill Baumgartner case report textual entity conclusion section The section labelled 'conclusion' in a typical scientific journal article. A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document. PERSON: Bill Baumgartner concluding remarks conclusion conclusions findings summary conclusion section conflict of interest section The section labelled 'conflict of interest statement' in a typical scientific journal article. A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document. PERSON: Bill Baumgartner authors' disclosures of potential conflicts of interest competing financial interests competing interests conflict of interest conflict of interest statement conflict of interests conflicts of interest declaration of competing interest declaration of competing interests declaration of interest declaration of interests disclosure of conflict of interest disclosure of potential conflicts of interest duality of interest statement of interest conflict of interest section conflict of interest statement SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document. PERSON: Bill Baumgartner conflict of interest textual entity consent section The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/) A part of a document about the consent process that was used to enroll patients in a study. PERSON: Bill Baumgartner consent consent section consent textual entity From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal. A textual entity that documents the consenting process used to enroll patients in a study. PERSON: Bill Baumgartner consent textual entity ethical approval section The section labelled 'ethical approval' in a typical scientific journal article. A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis. PERSON: Bill Baumgartner ethical approval ethical requirements ethics ethics statement ethical approval section ethical approval textual entity From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review. A textual entity that documents the ethical approval of some study design. PERSON: Bill Baumgartner ethical approval textual entity figures section The section labelled 'figures' in a typical scientific journal article. A part of a document that contains one or more figures. PERSON: Bill Baumgartner figures figures section funding source declaration section The section labelled 'funding' in a typical scientific journal article. A part of a document used to detail information regarding the source of funding used in support of the generation of the document content. PERSON: Bill Baumgartner financial support funding funding information funding sources funding statement funding/support grants role of the funding source source of funding sources of funding study funding funding source declaration section funding souce declaration textual entity From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication. A textual entity documenting the source of funding that supported some study. PERSON: Bill Baumgartner funding source declaration textual entity future directions section The section labelled 'future directions' in a typical scientific journal article. A part of a document detailing extensions of the described work that may be implemented at some future point in time. PERSON: Bill Baumgartner future challenges future considerations future developments future directions future outlook future perspectives future plans future prospects future research future research directions future studies future work outlook future directions section future directions textual entity Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members. A textual entity expressing ideas regarding future work relevant to work described in a document that could be done. PERSON: Bill Baumgartner future directions textual entity genome announcement section The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/) A document part announcing the publication of a novel draft genome sequence. PERSON: Bill Baumgartner genome announcement genome announcement section genome announcement textual entity Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB). A textual entity that describes the generation and public release of a novel, draft genome sequence. PERSON: Bill Baumgartner genome announcement textual entity keyword textual entity From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): Exon orthology; alternative splicing; exon duplication; intron-exon structure. A textual entity listing keywords indicating the major theme(s) of a document. PERSON: Bill Baumgartner keyword textual entity keywords section The section labelled 'keywords' in a typical scientific journal article. A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed. PERSON: Bill Baumgartner keywords keywords section study limitations section The section labelled 'limitations' in a typical scientific journal article. A part of a document about biases or short comings related to the study design and execution. PERSON: Bill Baumgartner limitations study limitations Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) study limitations section study limitations textual entity Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out. A textual entity addressing a shortcoming or bias of a study design or execution. PERSON: Bill Baumgartner Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) study limitations textual entity materials section The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/) A part of a document about the materials required to reproduce the content of the document. PERSON: Bill Baumgartner materials materials section notes section The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc. PERSON: Bill Baumgartner notes notes section patients section The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/) A part of a document about the patients that participated in a study. PERSON: Bill Baumgartner patients section patients textual entity Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred. A textual entity expressing information regarding the patients used in a study. PERSON: Bill Baumgartner patients textual entity pre-publication history section The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/) A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors. PERSON: Bill Baumgartner notice of republication pre-publication history pre-publication history section pre-publication history textual entity From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): The pre-publication history for this paper can be accessed here: http://www.biomedcentral.com/1471-2253/13/33/prepub A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information. PERSON: Bill Baumgartner pre-publication history textual entity related work section The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/) A part of a document about work in other publications that is relevant to the content of the document. PERSON: Bill Baumgartner related literature related work related work section related work textual entity Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015). A textual entity that discusses work from other publications and expresses their relevancy to the content of a document. PERSON: Bill Baumgartner related work textual entity requirements section The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource. PERSON: Bill Baumgartner requirements requirements section requirements textual entity From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): • Operating systems: Platform independent • Programming language: Matlab, R, Python • Other requirements: None • License: GNU GPL v3 • Any restrictions to use by non-academics: None A textual entity that expresses the requirements necessary to use a resource, e.g. software. PERSON: Bill Baumgartner requirements textual entity statistical analysis textual entity From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant. A textual entity documenting statistical analysis tools and techniques employed. PERSON: Bill Baumgartner statistical analysis textual entity statistical analysis section The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/) A part of the document used to describe the statistical methodologies employed in the work presented in the document. PERSON: Bill Baumgartner statistical analysis statistical analysis section tables section The section labelled 'tables' in a typical scientific journal article. A part of a document that contains one or more tables. PERSON: Bill Baumgartner tables tables section An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail. Mathias Brochhausen postal code A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region. Mathias Brochhausen Postal delivery route A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes. Mathias Brochhausen ZIP code zone improvement plan code database extract, transform, and load process A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second. Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output. PERSON:Alan Ruttenberg ETL WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load database extract, transform, and load process descriptive data section A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made. PERSON: Chen Yang PERSON: Jie Zheng https://www.equator-network.org/reporting-guidelines/prisma/ ONE ontology descriptive data section additional results section A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.) PERSON: Chen Yang PERSON: Jie Zheng https://www.equator-network.org/reporting-guidelines/consort/ https://www.equator-network.org/reporting-guidelines/prisma/ https://www.equator-network.org/reporting-guidelines/strobe/ ONE ontology additional results section research participants section A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.). PERSON: Chen Yang PERSON: Jie Zheng https://www.equator-network.org/reporting-guidelines/consort/ https://www.equator-network.org/reporting-guidelines/prisma/ https://www.equator-network.org/reporting-guidelines/strobe-nut/ ONE ontology research participants section measurement methods section A methods section that describes details of data assessment methods (data measurement). PERSON: Chen Yang PERSON: Jie Zheng https://www.equator-network.org/reporting-guidelines/strobe/ ONE ontology measurement methods section research settings section A document part that describes the physical/social/cultural conditions around a research trial. PERSON: Chen Yang PERSON: Jie Zheng https://www.ncbi.nlm.nih.gov/books/NBK262175/ ONE ontology research settings section study bias section A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others. PERSON: Chen Yang PERSON: Jie Zheng DOI: 10.1097/PRS.0b013e3181de24bc ONE ontology study bias section graphical abstract An abstract that is pictorial summary of the main findings described in the document. PERSON: Jie Zheng PERSON: Tim Beck visual abstract https://www.elsevier.com/authors/journal-authors/graphical-abstract Biomedical literature NLP project graphical abstract A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistantly identify oneself as a human researcher or contributor. "You can connect your iD with your professional information — affiliations, grants, publications, peer review, and more. You can use your iD to share your information with other systems, ensuring you get recognition for all your contributions, saving you time and hassle, and reducing the risk of errors." [https://orcid.org/] This class was originally defined in Apollo_SV (http://purl.obolibrary.org/obo/APOLLO_SV_00000496) but due to it being more in scope of IAO, it was decided to add it to IAO and deprecate its Apollo_SV equivalent. (2022-10-25) http://orcid.org/0000-0002-1595-3213 ORCID ID ORCiD Open Researcher and Contributor ID Open Researcher and Contributor Identifier https://orcid.org/ https://github.com/information-artifact-ontology/IAO/issues/259 ORCID identifier identifier An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. Justin Whorton Mathias Brochhausen Mathias Brochhausen proper name https://github.com/information-artifact-ontology/IAO/issues/237 Mathias Brochhausen Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB) identifier alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems An information content entity that is a fundamental unit in a written language. Justin Whorton http://en.wikipedia.org/wiki/Grapheme https://github.com/information-artifact-ontology/IAO/issues/237 Mathias Brochhausen Grapheme is not about anything and hence is likely to not be an information content entity. If a new subclass of GDC for information structure entities is created it should move there. grapheme A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. Justin Whorton Mathias Brochhausen Mathias Brochhausen dubbing process naming https://github.com/information-artifact-ontology/IAO/issues/237 Mathias Brochhausen identifier creating process A personal name is a proper name identifying an individual person. An identifier referring to an individual entity that is ascribed personhood by the user of the identifier. Justin Whorton Mathias Brochhausen Mathias Brochhausen http://en.wikipedia.org/wiki/Personal_name https://github.com/information-artifact-ontology/IAO/issues/237 Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name) Personal names to not include names of fictional characters, e.g. Sherlock Holmes. Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB) personal name A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name Justin Whorton Mathias Brochhausen first name http://en.wikipedia.org/wiki/Given_name https://github.com/information-artifact-ontology/IAO/issues/237 given name An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children. Justin Whorton Mathias Brochhausen last name surname http://en.wikipedia.org/wiki/Family_name https://github.com/information-artifact-ontology/IAO/issues/237 family name An information content entity that is a collection of other information content entities that has been created to identify or annotate core ideas of a specified domain, and where the intention of its creators is that the aggregated entities have a one-to-one correspondence with entities in reality outside the aggregate. An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things. Alan Ruttenberg Justin Whorton Mathias Brochhausen Mathias Brochhausen code map code system codeset coding system controlled vocabulary https://github.com/information-artifact-ontology/IAO/issues/237 Alan Ruttenberg Clint Dowland Matt Diller Sarah Bost William R. Hogan Code sets might include non-entities/things (e.g. missing thumbs). Does not imply absence vs. presence of any taxonomy. Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities. Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean). For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs). For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets. Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain. The information content entities do not denote each other. code set Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived. Mathias Brochhausen The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012). Reinach clearly does not imply that a command that does not fulfill its prupose would not be a command. Thanks to W.R. Hogan for finding the Reinach quote. social act A social act that creates or revokes a deontic role. Mathias Brochhausen deontic declaration ontology module I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. ontology file This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. ontology module base ontology module An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. base ontology module editors ontology module An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. source ontology module editors ontology module main release ontology module An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module main release ontology module bridge ontology module An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. bridge ontology module import ontology module A subset ontology module that is intended to be imported from another ontology. TODO: add axioms that indicate this is the output of a module extraction process. import file import ontology module subset ontology module An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. ontology slim subset ontology subset ontology module curation subset ontology module A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. curation subset ontology module analysis ontology module An ontology module that is intended for usage in analysis or discovery applications. analysis subset ontology module single layer ontology module A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. ribbon subset single layer subset ontology module exclusion subset ontology module A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. antislim exclusion subset ontology module external import ontology module An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. external import external import ontology module species subset ontology module A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. taxon subset species subset ontology module reasoned ontology module An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. reasoned ontology module generated ontology module An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process generated ontology module template generated ontology module An ontology module that is automatically generated from a template specification and fillers for slots in that template. template generated ontology module taxonomic bridge ontology module taxonomic bridge ontology module ontology module subsetted by expressivity ontology module subsetted by expressivity obo basic subset ontology module A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports obo basic subset ontology module ontology module subsetted by OWL profile ontology module subsetted by OWL profile EL++ ontology module EL++ ontology module An infectious disposition to become part of a disorder only in organisms whose defenses are compromised. Albert Goldfain Alexander Diehl Lindsay Cowell opportunitistic pathogenic disposition The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host. This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin). opportunistic infectious disposition An infectious disposition to become part of a disorder in organisms that have intact defenses. Albert Goldfain Alexander Diehl Lindsay Cowell A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts. A quote from page 3 of Mandell's "Principles and Practice of Infectious Diseases" (Sixth edition): "It is useful to distinguish "principal" pathogens, which regularly cause disease in some proportion of susceptible individuals with apparently intact defense systems, from other potentially pathogenic microorganisms. ... even for most organisms classified as principal pathogens, for example, Staphylococcus aureus and the pneumococcus, some impairment or local breakdown in normal host defense mechanisms must occur for these bacteria to cause disease. ... Thus, it seems clear that the capacity of certain microorganisms to cause disease in seemingly uncompromised human hosts on a regular basis reflects some fundamental difference in their virulence capabilities from those of opportunists and the more numerous commensal species that rarely, if ever, cause disease." primary infectious disposition A disposition to initiate processes that result in a disorder. Albert Goldfain Alexander Diehl Lindsay Cowell pathogenicity A pathogenic disposition is realized in processes that create a disorder. The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition. By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition. pathogenic disposition A pathogenic disposition that inheres in an organism and is a disposition for that organism (1) to be transmitted to a host, (2) to establish itself in the host, (3) to initiate processes that result in a disorder in the host, and (4) to become part of that disorder. Albert Goldfain Alexander Diehl Lindsay Cowell The disposition is realized in a process that has as part a transmission process, an establishment in host process, a process that results in a disorder, and a process in which the bearer of the disposition becomes part of that disorder. The infectious disposition has a complementary disposition that inheres in an organism and is the capability to be host to an organism with an infectious disposition and to undergo processes initiated by that infectious organism that result in a disorder. infectious disposition An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host. Albert Goldfain Alexander Diehl Lindsay Cowell An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis. zoonotic disposition An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host. Albert Goldfain Alexander Diehl Lindsay Cowell An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis. reverse zoonotic disposition An organism that has immunocompetence. Albert Goldfain Alexander Diehl Lindsay Cowell immunocompetent organism A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process. Albert Goldfain Alexander Diehl Lindsay Cowell The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening. infectious agent transmissibility A quality that inheres in an infectious agent and is the liklihood that the infectious disposition will be realized upon exposure of a susceptible organism. Albert Goldfain Alexander Diehl Lindsay Cowell This quality is measured by the proportion of exposed who become infected. infectivity A quality that inheres in an infectious agent and is the degree to which realizations of the infectious disease caused by the infectious agent become severe or fatal. Albert Goldfain Alexander Diehl Lindsay Cowell This quality is measured by the proportion of clinically apparent cases that are severe or fatal. virulence A quality that inheres in an entity and is the degree to which it can be harmed by another entity. Albert Goldfain Alexander Diehl Lindsay Cowell Low susceptibility is often referred to as resistance. In this sense, resistance is a quality. susceptibility A quality that inheres in an organism population and is the number of realizations of an infectious disease for which the infectious disease course begins during a specified period of time. Albert Goldfain Alexander Diehl Lindsay Cowell A particular instance of infectious disease incidence will depend on a type of infectious disease, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure. infectious disease incidence A quality that inheres in an organism population and is the number of organisms in the population that become infected with an infectious agent during a specified period of time. Albert Goldfain Alexander Diehl Lindsay Cowell A particular instance of infection incidence will depend on a type of infectious agent, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure. infection incidence A quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time and in whom the infectious disease begins during the specified period of time. Albert Goldfain Alexander Diehl Lindsay Cowell cumulative incidence of infectious disease An instance of infectious disease incidence proportion is measured by dividing a measure of an instance of infectious disease incidence by the number of members of the population in which the infectious disease course had not begun at the beginning of the specified period of time over which the incidence was measured. infectious disease incidence proportion A quality that inheres in an organism population and is the proportion of members of the population not infected at the beginning of a specified period of time who become infected during the specified period of time. Albert Goldfain Alexander Diehl Lindsay Cowell cumulative incidence of infection An instance of infection incidence proportion is measured by dividing a measure of an instance of infection incidence by the number of members of the population not infected at the beginning of the specified period of time over which the incidence was measured. infection incidence proportion A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time. Albert Goldfain Alexander Diehl Lindsay Cowell An instance of infectious disease incidence rate is measured by dividing a measure of an instance of the infectious disease incidence proportion by the length of the period of time over which the incidence was measured. infectious disease incidence rate A quality that inheres in an organism population and is the infection incidence proportion per unit time. Albert Goldfain Alexander Diehl Lindsay Cowell An instance of infection incidence rate is measured by dividing a measure of an instance of infection incidence proportion by the length of the period of time over which the incidence was measured. infection incidence rate A quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time. Albert Goldfain Alexander Diehl Lindsay Cowell Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease prevalence will depend on a type of infectious disease, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. infectious disease prevalence A quality that inheres in an organism population and is the number of organisms in the population infected with an infectious agent at a specified time. Albert Goldfain Alexander Diehl Lindsay Cowell Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infection prevalence will depend on a type of infectious agent, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. infection prevalence A quality that inheres in an organism population and is the number of organisms in the population who have, at any point during their lives, been bearers of an infectious disease and experienced realization of the disease. Albert Goldfain Alexander Diehl Lindsay Cowell Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease lifetime prevalence will depend on a type of infectious disease and a population. Actual measures of prevalence are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. infectious disease lifetime prevalence A quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for an infectious agent in their serum at a specified time. Albert Goldfain Alexander Diehl Lindsay Cowell Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious agent seroprevalence will depend on a type of infectious agent and a population. Actual measures of seroprevalence are based only on tested individuals and usually specify a geographic location. Other constraints may include population demographics. infectious agent seroprevalence A quality that inheres in an organism population and is the per capita number of deaths in the population resulting from an infectious disease over a specified period of time. Albert Goldfain Alexander Diehl Lindsay Cowell A particular instance of infectious disease mortality rate will depend on a type of infectious disease and a population. Actual measures of mortality rate are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. Mortality rate is typically expressed in units of deaths per 1000 individuals per year. infectious disease mortality rate A quality that inheres in an organism population in virtue of the fact that infections of the type that causes an infectious disease are maintained in the population via intra-population transmission or by transmission from a local reservoir. Albert Goldfain Alexander Diehl Lindsay Cowell A particular instance of infectious disease endemicity will depend on a type of infectious agent and a population. The population may be specified by temporal, geographic, or demographic constraints. Infectious diseases that are typical or common to a particular population are referred to as endemic. infectious disease endemicity A quality that inheres in an organism population by virtue of the fact that realizations of an infectious disease occur in the population with a fluctuating prevalence. Albert Goldfain Alexander Diehl Lindsay Cowell Sporadic quality of infectious disease is relational to previous prevalence of the disease. infectious disease sporadicity An aggregate of organisms of the same Species. Albert Goldfain Alexander Diehl Lindsay Cowell The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age. organism population A material entity with a pathogenic disposition. Albert Goldfain Alexander Diehl Lindsay Cowell pathogen An infectious agent with a primary infectious disposition. Albert Goldfain Alexander Diehl Lindsay Cowell principal pathogen primary pathogen An organism bearing a host role. Albert Goldfain Alexander Diehl Lindsay Cowell host An organism that has an infectious disposition. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent A process that attenuates an immune response. Albert Goldfain Alexander Diehl Lindsay Cowell immunosuppression A disposition that is the ability to mount a normal immune response. Albert Goldfain Alexander Diehl Lindsay Cowell The disposition inheres in a bearer in virtue of the fact that the bearer has all canonical immune system components and none are disordered. The disposition is realized in a successful immune response. immunocompetence An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission. Albert Goldfain Alexander Diehl Lindsay Cowell The disposition is realized in a direct, horizontal transmission process between members of the same Species. communicability An establishment of localization process in which a material entity reaches a site in an organism in which it can survive, grow, multiply, or mature. Requested addition of this term to the GO. Albert Goldfain Alexander Diehl Lindsay Cowell An organism begins bearing a particular host role as soon as the extended organism contains the relevant material entity, regardless of that entity's location in the extended organism. An establishment process is any process by which the entity reaches a location in the extended organism in which it can persist and continue its lifecycle. For example, an organism is host to a virus as soon as any part of the extended organism is occupied by virus particles. During an establishment process, virus particles enter host cells of the relevant type, and viral DNA is integrated into host DNA. establishment of localization in host A process by which a disorder comes into existence. Albert Goldfain Alexander Diehl Lindsay Cowell appearance of disorder A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism. Albert Goldfain Alexander Diehl Lindsay Cowell host role An infectious agent with an opportunistic infectious disposition. Albert Goldfain Alex Diehl Lindsay Cowell opportunist opportunistic pathogen A pathogen transmission process in which a pathogen is transmitted from one host to another of the same Species, and the two hosts are not in a parent-child relationship. Lindsay Cowell horizontal pathogen transmission process Intentionality is the fundamental quality of conscious mental processes of always having content, of being directed towards, or about something. intentionality A bodily quality is a quality that inheres in some extended organism. bodily quality A mental quality is a bodily quality that inheres in those structures of the extended organism that are essential for mental functioning. mental quality http://purl.obolibrary.org/obo/MF.owl George Gkoutos 2011-04-14T01:03:39Z "Behaviour related to the activity which primary purpose is the sexual reproduction." [NBO:GVG] behavior_ontology sexual activity Mus musculus William R. Hogan House mouse Mus musculus Virus Viruses Poxviridae Chordopoxvirinae Orthopoxvirus Mirela L Vasconcelos monkey pox virus Monkeypox virus Variola virus H5N1 subtype of Influenza A virus H5N1 subtype GC_ID:1 ncbi_taxonomy Herpesviridae GC_ID:1 ncbi_taxonomy Alphaherpesvirinae GC_ID:1 ncbi_taxonomy Simplexvirus HSV-1 HSV1 GC_ID:1 Herpes simplex virus type 1 ncbi_taxonomy Herpes simplex virus 1 Human Herpesvirus-1 Human herpesvirus 1 Human herpesvirus type 1 herpes simplex virus 1 HSV-1 herpes simplex virus HSV-1 herpes simplex virus type 1 HSV-1 herpes simplex virus type 1 HSV1 herpes simplex virus type-1 HSV-1 Human alphaherpesvirus 1 HSV-1 HSV1 Herpes simplex virus type 1 Herpes simplex virus 1 Human Herpesvirus-1 Human herpesvirus 1 Human herpesvirus type 1 herpes simplex virus 1 HSV-1 herpes simplex virus HSV-1 herpes simplex virus type 1 HSV-1 herpes simplex virus type 1 HSV1 herpes simplex virus type-1 HSV-1 HSV2 GC_ID:1 Herpes simplex virus type 2 (HSV-2) ncbi_taxonomy Herpes simplex virus (type 2) Herpes simplex virus 2 Herpes simplex virus II Herpes simplex virus type 2 Human herpesvirus 2 herpes simplex virus type 2 HSV-2 Human alphaherpesvirus 2 HSV2 Herpes simplex virus type 2 (HSV-2) Herpes simplex virus (type 2) Herpes simplex virus 2 Herpes simplex virus II Herpes simplex virus type 2 Human herpesvirus 2 herpes simplex virus type 2 HSV-2 GC_ID:1 ncbi_taxonomy Varicellovirus HHV-3 VZV GC_ID:1 Varicella-zoster virus ncbi_taxonomy Human alphaherpesvirus 3 Human herpes virus 3 Varicella Zoster Virus varicella zoster virus VZV varicella-zoster virus VZV Human herpesvirus 3 HHV-3 VZV Varicella-zoster virus Human alphaherpesvirus 3 Human herpes virus 3 Varicella Zoster Virus varicella zoster virus VZV varicella-zoster virus VZV NCBITaxon:44156 PRV GC_ID:1 Pseudorabies virus ncbi_taxonomy Alphaherpesvirus pseudorabies virus PRV Aujeszky's disease virus Pseudorabies Virus PRV Suid herpesvirus type 1 Suid herpesvirus 1 PRV Pseudorabies virus Alphaherpesvirus pseudorabies virus PRV Aujeszky's disease virus Pseudorabies Virus PRV Suid herpesvirus type 1 GC_ID:1 hepatitis B-type viruses ncbi_taxonomy Hepadnaviridae hepatitis B-type viruses GC_ID:1 mammalian hepatitis B-type viruses ncbi_taxonomy Orthohepadnavirus mammalian hepatitis B-type viruses HBV GC_ID:1 ncbi_taxonomy Human hepatitis B virus hepatitis B virus (HBV) hepatitis B virus HBV hepatitis B virus, HBV human hepatitis B virus HBV Hepatitis B virus HBV Human hepatitis B virus hepatitis B virus (HBV) hepatitis B virus HBV hepatitis B virus, HBV human hepatitis B virus HBV GC_ID:11 ncbi_taxonomy Escherichia coli O157 Aedini GC_ID:11 ncbi_taxonomy canis group GC_ID:11 phagocytophila group ncbi_taxonomy phagocytophilum group phagocytophila group Mirela L Vasconcelos Reoviridae Mirela L Vasconcelos Rotaviruses Rotavirus Togaviridae GC_ID:1 arboviruses group A ncbi_taxonomy Alphaviridae Alphavirus Alphavirus arboviruses group A Alphaviridae GC_ID:1 ncbi_taxonomy Barmah Forest virus GC_ID:1 ncbi_taxonomy Eastern equine encephalomyelitis virus eastern equine encephalomyelitis EEE eastern equine encephalomyelitis virus EEEV Eastern equine encephalitis virus Eastern equine encephalomyelitis virus eastern equine encephalomyelitis EEE eastern equine encephalomyelitis virus EEEV RRV GC_ID:1 ncbi_taxonomy Ross River virus RRV GC_ID:1 ncbi_taxonomy Western equine encephaliomyelitis virus Western equine encephalomyelitis virus Western equine encephalitis virus Western equine encephaliomyelitis virus Western equine encephalomyelitis virus GC_ID:1 ncbi_taxonomy Rubivirus GC_ID:1 ncbi_taxonomy Rubella virus Flaviviridae GC_ID:1 arboviruses group B ncbi_taxonomy Flavivirus Flavivirus arboviruses group B Dengue virus group Dengue virus 1 Dengue virus 2 Dengue virus 3 Dengue virus 4 GC_ID:1 ncbi_taxonomy Japanese encephalitis viruses Japanese encephalitis virus group Japanese encephalitis viruses GC_ID:1 ncbi_taxonomy Japanese encephalitis Japanese encephalitis (JE) virus Japanese encephalitis virus JE Japanese encephalitis virus JEV Japanese encephalitis virus Japanese encephalitis Japanese encephalitis (JE) virus Japanese encephalitis virus JE Japanese encephalitis virus JEV GC_ID:1 ncbi_taxonomy Murray Valley encephalitis virus NCBITaxon:64321 GC_ID:1 ncbi_taxonomy Saint Louis encephalitis virus St. Louis encephalitis virus SLEV St. Louis encephalitis virus Saint Louis encephalitis virus St. Louis encephalitis virus SLEV WNV GC_ID:1 ncbi_taxonomy West Nile virus WNV GC_ID:1 ncbi_taxonomy Flavivirus powassan Powassan virus Flavivirus powassan YFV GC_ID:1 ncbi_taxonomy Flavivirus febricis yellow fever virus YFV Yellow fever virus YFV Flavivirus febricis yellow fever virus YFV Mirela L Vasconcelos Hepatitis C virus group Hepatitis C viruses Hepatitis C-like viruses Hepacivirus Mirela L Vasconcelos hepatitis C virus HCV human hepatitis C virus human hepatitis C virus HCV human hepatitis virus C HCV post-transfusion hepatitis non A non B virus Hepatitis C virus Coronaviridae http://purl.obolibrary.org/obo/obi.owl Coronaviridae Mirela L Vasconcelos Chlamydia/Chlamydophila group GC_ID:11 ncbi_taxonomy pseudomallei group Mononegavirales Paramyxoviridae Paramyxovirinae GC_ID:1 ncbi_taxonomy Mumps virus Mirela L Vasconcelos Morbilliviruses Morbillivirus Measles virus Mirela L Vasconcelos Pneumovirinae Pneumoviridae Mirela L Vasconcelos Pneumovirus Filoviridae MBG GC_ID:1 ncbi_taxonomy Lake Victoria marburgvirus Marburg virus MBG Marburg marburgvirus MBG Lake Victoria marburgvirus Marburg virus MBG Mirela L Vasconcelos Rhabdoviridae Mirela L Vasconcelos Lyssavirus Mirela L Vasconcelos Rabies virus Rabies lyssavirus Orthomyxoviridae Influenza A virus GC_ID:11 PMID:9734038 ncbi_taxonomy spotted fever group GC_ID:11 ncbi_taxonomy typhus group H1N1 subtype of Influenza A virus H1N1 subtype H2N2 subtype of Influenza A virus H2N2 subtype Mirela L Vasconcelos Influenza virus type B Influenza B virus Mirela L Vasconcelos GC_ID:1 ncbi_taxonomy Bunyaviridae Bunyaviridae GC_ID:1 ncbi_taxonomy Bunyavirus Bunyaviruses Orthobunyavirus Bunyavirus Bunyaviruses GC_ID:1 ncbi_taxonomy Bunyavirus la crosse La Crosse virus Bunyavirus la crosse GC_ID:1 ncbi_taxonomy Bunyavirus snowshoe hare Snowshoe hare bunyavirus Snowshoe hare virus Bunyavirus snowshoe hare Snowshoe hare bunyavirus Mirela L Vasconcelos Phleboviruses Phlebovirus Mirela L Vasconcelos Rift Valley fever virus GC_ID:1 ncbi_taxonomy Hantaviurs Hantavirus Hantaviurs GC_ID:1 ncbi_taxonomy Arenaviridae GC_ID:1 ncbi_taxonomy Junin arenavirus Junin virus Junn mammarenavirus Junin mammarenavirus Junin arenavirus Junin virus Junn mammarenavirus GC_ID:1 ncbi_taxonomy Lassa virus Lassa mammarenavirus Lassa virus GC_ID:1 ncbi_taxonomy Machupo virus Machupo mammarenavirus Machupo virus Retroviridae Lentivirinae Lentivirus Primate immunodeficiency viruses Primate lentivirus group HIV-1 Human immunodeficiency virus type 1 human immunodeficiency virus 1 HIV-1 human immunodeficiency virus HIV-1 human immunodeficiency virus type 1 HIV 1 human immunodeficiency virus type 1 HIV-1 human immunodeficiency virus type 1 HIV1 human immunodeficiency virus type 1, HIV-1 human immunodeficiency virus type I HIV-1 human immunodeficiency virus type-1 HIV-1 human immunodeficiency virus-1 HIV-1 Human immunodeficiency virus 1 HIV type 2 HIV-2 Human immunodeficiency virus type 2 Human immunodeficiency virus-2 human immunodeficiency virus type 2 HIV-2 human immunodeficiency virus type 2, HIV-2 Human immunodeficiency virus 2 Teleostomi bony vertebrates Euteleostomi GC_ID:11 ncbi_taxonomy Brucellaceae Breed et al. 1957 Brucellaceae Brucellaceae Breed et al. 1957 GC_ID:11 PMID:16280474 ncbi_taxonomy Coxiella group Coxiellaceae Coxiella group GC_ID:11 PMID:16280474 ncbi_taxonomy Legionellaceae group Legionellales Garrity et al. 2005 Legionellales Legionellaceae group Legionellales Garrity et al. 2005 NCBITaxon:119063 GC_ID:11 PMID:16403855 ncbi_taxonomy Burkholderia group Burkholderiaceae Burkholderia group GC_ID:1 ncbi_taxonomy Enoplea NCBITaxon:27837 GC_ID:1 ncbi_taxonomy Adenophorea Chromadorea Adenophorea H3N2 subtype of Influenza A virus H3N2 subtype H7N2 subtype of Influenza A virus H7N2 subtype H7N7 subtype of Influenza A virus H7N7 subtype H5N2 subtype of Influenza A virus H5N2 subtype Mirela L Vasconcelos Caliciviridae Picornaviridae Enterovirus Ecdysozoa Human poliovirus type 1 Poliovirus type 1 poliovirus type 1 PV1 Human poliovirus 1 Human poliovirus type 3 Poliovirus type 3 Human poliovirus 3 Mirela L Vasconcelos Hepatovirus Mirela L Vasconcelos Hepatitis A virus Hepatovirus A Mirela L Vasconcelos Aphthovirus Mirela L Vasconcelos Foot and mouth disease virus foot and mouth disease virus FMDV foot-and-mouth disease virus FMDV Foot-and-mouth disease virus GC_ID:1 ncbi_taxonomy Nipah virus Nipah henipavirus Nipah virus Mirela L Vasconcelos Alphaproteobacteraeota purple bacteria purple bacteria and relatives purple non-sulfur bacteria purple photosynthetic bacteria purple photosynthetic bacteria and relatives Proteobacteria Mirela L Vasconcelos Proteobacteria gamma subdivision Purple bacteria, gamma subdivision gamma proteobacteria gamma subdivision gamma subgroup Gammaproteobacteria Gram-postive bacterium Firmicutes HEV GC_ID:1 ncbi_taxonomy Hepatitis E virus HEV Hepatitis E virus HEV Hepatitis E virus HEV Mirela L Vasconcelos Hepatitis D virus hepatitis delta virus HDV Hepatitis delta virus Dengue virus Staphylococcus Aurococcus Staphylococcus Mirela L Vasconcelos Vibrio cholerae serogroup O1 Vibrio cholerae O1 Staphylococcus aureus Micrococcus aureus Micrococcus pyogenes Staphlococcus pyogenes citreus Staphylococcus pyogenes aureus Streptococcus aureus Staphylococcus aureus GC_ID:1 ncbi_taxonomy Conoidasida Mirela L Vasconcelos respiratory syncytial virus RS respiratory syncytial virus RS virus respiratory syncytial virus RSV Respiratory syncytial virus Mirela L Vasconcelos Streptococcaceae Mirela L Vasconcelos Streptococcus GC_ID:1 ncbi_taxonomy Charophyta/Embryophyta group charophyte/embryophyte group Streptophytina Charophyta/Embryophyta group charophyte/embryophyte group Mirela L Vasconcelos Diplococcus pneumoniae Micrococcus pneumoniae Streptococcus pneumoniae GC_ID:1 PMID:22839753 PMID:25450099 ncbi_taxonomy Archosauria-Testudines Testudines + Archosauria group Archelosauria Archosauria-Testudines Testudines + Archosauria group Middle East respiratory syndrome coronavirus Dipnotetrapodomorpha Mirela L Vasconcelos Vibrionaceae group Vibrionales Mirela L Vasconcelos Pasteruellaceae group Pasteurellales GC_ID:11 PMID:11075904 PMID:11542017 PMID:16558735 PMID:1917844 PMID:23908650 ncbi_taxonomy spirochetes Spirochaetales spirochetes GC_ID:11 PMID:23908650 ncbi_taxonomy Treponemataceae Spirochaetaceae Treponemataceae GC_ID:11 PMID:24744012 PMID:8863409 PMID:8863416 ncbi_taxonomy Relapsing Fever Borrelia Borrelia Relapsing Fever Borrelia Bacillales Bacillus Mirela L Vasconcelos Coxsackievirus A Enterovirus EV-A Human coxsackievirus A Human enterovirus A Enterovirus A Enterovirus EV-C Human enterovirus C Poliovirus Enterovirus C Enterovirus D Mirela L Vasconcelos Bacillus cereus var. anthracis Bacteridium anthracis anthrax anthrax bacterium Bacillus anthracis Mirela L Vasconcelos Norwalk-like viruses Norovirus GC_ID:1 PMID:11743200 PMID:11791233 ncbi_taxonomy Boreotheria Boreoeutheria Boreoeutheria Boreotheria NCBITaxon:92178 GC_ID:1 PMID:10701576 Trichinella T5 Trichinella sp. T5 ncbi_taxonomy Trichinella murrelli Trichinella T5 Trichinella sp. T5 GC_ID:1 ncbi_taxonomy Dorylaimia GC_ID:1 true yeasts ncbi_taxonomy Saccharomycotina true yeasts GC_ID:1 ncbi_taxonomy Euascomycota Pezizomycotina Euascomycota NCBITaxon:147540 GC_ID:1 ncbi_taxonomy Loculoascomycetes Plectomycetes bitunicate ascomycetes Eurotiomycetes Loculoascomycetes Plectomycetes bitunicate ascomycetes Rhinovirus A Rhinovirus A NCBITaxon:69207 GC_ID:11 PMID:26643615 ncbi_taxonomy Anaerobacter Clostridium Anaerobacter NCBITaxon:29368 GC_ID:11 PMID:10028279 PMID:15244052 ncbi_taxonomy Bacillus botulinus Bacillus putrificus Botulobacillus botulinus Clostridium putrificum Ermengemillus botulinus Pacinia putrifica Clostridium botulinum Bacillus botulinus Bacillus putrificus Botulobacillus botulinus Clostridium putrificum Ermengemillus botulinus Pacinia putrifica Mirela L Vasconcelos Bacillus difficilis Clostridium difficile Peptoclostridium difficile Clostridioides difficile GC_ID:11 ncbi_taxonomy Bacillus tetani Clostridium tetani Bacillus tetani GC_ID:1 ncbi_taxonomy Clavispora/Candida clade GC_ID:1 ducks, geese, chickens, fowl, quail, currasows and allies ncbi_taxonomy Galloanseri Galloanserae ducks, geese, chickens, fowl, quail, currasows and allies Galloanseri GC_ID:11 PMID:23961314 PMID:9019153 PMID:9734025 ncbi_taxonomy Microspironema Treponema Microspironema NCBITaxon:34383 GC_ID:1 ncbi_taxonomy Onygenales incertae sedis GC_ID:11 ncbi_taxonomy Microspironema pallidum Spirillum pallidum Spirochaeta pallida Spironema pallidum Treponema pallidum Microspironema pallidum Spirillum pallidum Spirochaeta pallida Spironema pallidum GC_ID:11 Treponema pallidum pallidum syphilis treponeme ncbi_taxonomy Treponema pallidum subsp. pallidum Treponema pallidum pallidum syphilis treponeme GC_ID:11 PMID:10408878 PMID:15709360 PMID:1713054 PMID:1899799 PMID:8427807 PMID:8782674 PMID:9226919 PMID:9542083 ncbi_taxonomy Listerella Listeria Listerella GC_ID:11 PMID:8782698 ncbi_taxonomy Listeria bulgarica Listeria monocytogenes subsp. perhaemolytica Listeria perhaemolytica Listeria ivanovii Listeria bulgarica Listeria monocytogenes subsp. perhaemolytica Listeria perhaemolytica NCBITaxon:1634566 GC_ID:11 PMID:17773427 PMID:1906732 PMID:8782698 ncbi_taxonomy Bacterium monocytogenes Bacterium monocytogenes hominis Corynebacterium infantisepticum Corynebacterium parvulum Erysipelothrix monocytogenes Listerella hepatolytica Listeria momocytogenes Lysteria monocytogenes Listeria monocytogenes Bacterium monocytogenes Bacterium monocytogenes hominis Corynebacterium infantisepticum Corynebacterium parvulum Erysipelothrix monocytogenes Listerella hepatolytica Listeria momocytogenes Lysteria monocytogenes Mirela L Vasconcelos Plasmodiidae NCBITaxon:1644 NCBITaxon:47986 GC_ID:11 PMID:1736964 Listeria grayi grayi ncbi_taxonomy Listeria grayi murrayi Listeria grayi subsp. grayi Listeria murrayi Murraya grayi Murraya grayi subsp. grayi Listeria grayi Listeria grayi grayi Listeria grayi murrayi Listeria grayi subsp. grayi Listeria murrayi Murraya grayi Murraya grayi subsp. grayi GC_ID:11 PMID:23908650 ncbi_taxonomy Borreliaceae GC_ID:11 PMID:23908650 ncbi_taxonomy Leptospiriales Leptospirales Leptospiriales GC_ID:11 ncbi_taxonomy Yersinia pseudotuberculosis complex GC_ID:11 PMID:19244447 Coryneform bacteria ncbi_taxonomy Corynebacteriaceae Coryneform bacteria GC_ID:1 ncbi_taxonomy Mammarenavirus GC_ID:1 ncbi_taxonomy Orthohepevirus GC_ID:1 ncbi_taxonomy Orthohepevirus A GC_ID:11 PMID:16014471 ncbi_taxonomy Treponemataceae Leptospiraceae Treponemataceae NCBITaxon:29512 NCBITaxon:29514 NCBITaxon:29516 GC_ID:11 PMID:10425768 PMID:1581182 PMID:19868121 PMID:9103653 ncbi_taxonomy Ancona Canela Jequitaia Leptospira Ancona Canela Jequitaia GC_ID:11 PMID:10425754 PMID:19661509 PMID:7547284 PMID:7547291 PMID:7547293 ncbi_taxonomy Corynebacterium GC_ID:11 PMID:7729671 ncbi_taxonomy Bacillus diphtheriae Bacterium diphtheriae Microsporon diphthericum Microsporon diphtheriticum Mycobacterium diphtheriae Pacinia loeffleri Corynebacterium diphtheriae Bacillus diphtheriae Bacterium diphtheriae Microsporon diphthericum Microsporon diphtheriticum Mycobacterium diphtheriae Pacinia loeffleri Actinomycetes High GC gram-positive bacteria Actinobacteria <class> Mycobacteriaceae Mycobacterium Lehmann and Neumann 1896 Mycobacterium GC_ID:11 ncbi_taxonomy Bacillus leprae Mycoplasma leprae Mycobacterium leprae Bacillus leprae Mycoplasma leprae Bacillus tuberculosis Bacterium tuberculosis Mycobacterium tuberculosis typus humanus Mycobacterium tuberculosis var. hominis Mycobacterium tuberculosis GC_ID:1 ncbi_taxonomy EEEV complex GC_ID:1 ncbi_taxonomy WEEV complex SFV complex Mirela L Vasconcelos PVC group Mirela L Vasconcelos Terrabacteria group Ebola-like virus Ebolavirus GC_ID:1 ncbi_taxonomy Marburg-like viruses Marburgvirus Marburg-like viruses Zaire ebolavirus Ebola virus Reston REBOV Reston Ebola virus Reston ebolavirus Ebolavirus Sudan SEBOV Sudan Ebola virus Sudan ebolavirus CIEBOV Côte d'Ivoire Ebola virus Côte d'Ivoire ebolavirus Ivory Coast ebolavirus Tai Forest ebolavirus Mirela L Vasconcelos Clostridia Mirela L Vasconcelos Clostridiales Mirela L Vasconcelos Clostridium cluster XI Peptostreptococcaceae Bacillaceae GC_ID:11 PMID:20212322 ncbi_taxonomy Listeriaceae Mirela L Vasconcelos Lactobacillales Mirela L Vasconcelos Clostridioides GC_ID:11 PMID:27620848 ncbi_taxonomy Yersiniaceae Mirela L Vasconcelos Rift Valley fever phlebovirus GC_ID:1 ncbi_taxonomy California encephalitis orthobunyavirus GC_ID:1 ncbi_taxonomy Guaroa orthobunyavirus GC_ID:11 PMID:11542086 PMID:12361288 PMID:16627635 PMID:1704793 PMID:19801389 ncbi_taxonomy Ampylobacter Campylobacter Ampylobacter Pancrustacea Mandibulata Influenzavirus A Mirela L Vasconcelos Influenzavirus B GC_ID:1 ncbi_taxonomy Bunyavirales GC_ID:1 ncbi_taxonomy Nairoviridae NCBITaxon:11571 GC_ID:1 ncbi_taxonomy Bunyaviridae Peribunyaviridae Bunyaviridae NCBITaxon:11592 GC_ID:1 ncbi_taxonomy Nairovirus Nairoviruses Orthonairovirus Nairovirus Nairoviruses NCBITaxon:11593 CCHFV GC_ID:1 ncbi_taxonomy Crimean Congo Hemorrhagic Fever virus Crimean-Congo haemorrhagic fever virus Crimean-Congo hemorrhagic fever nairovirus Crimean-Congo hemorrhagic fever virus Crimean-Congo hemorrhagic virus Crimean-Congo hemorrhagic fever orthonairovirus CCHFV Crimean Congo Hemorrhagic Fever virus Crimean-Congo haemorrhagic fever virus Crimean-Congo hemorrhagic fever nairovirus Crimean-Congo hemorrhagic fever virus Crimean-Congo hemorrhagic virus GC_ID:1 ncbi_taxonomy Coccidioides posadasii Bacteria Bacteria 'Actinobacteria' not Actinobacteria Cavalier-Smith 2002 Actinobacteria <phylum> GC_ID:11 PMID:11837318 PMID:26654112 ncbi_taxonomy Spirochaetae Spirochaetaeota Spirochaetes Spirochaetae Spirochaetaeota GC_ID:11 PMID:11837318 PMID:25288668 PMID:26654112 ncbi_taxonomy Spirochaetes Spirochaetia Spirochaetes Mirela L Vasconcelos Chlamydaeota Chlamydiae Mirela L Vasconcelos Chlamydiae Chlamydiia Mirela L Vasconcelos Neisseriales GC_ID:1 ncbi_taxonomy Diplomonadida group Fornicata Diplomonadida group Mirela L Vasconcelos Helicobacter Mirela L Vasconcelos Campylobacter pylori Campylobacter pylori subsp. pylori Campylobacter pyloridis Helicobacter nemestrinae Helicobacter pylori Mirela L Vasconcelos Campylobacterales Archaea NCBITaxon:261182 GC_ID:1 ncbi_taxonomy Sarcoptidia Psoroptidia Sarcoptidia SARS coronavirus H5N8 subtype of Influenza A virus H5N8 subtype GC_ID:11 PMID:8573514 ncbi_taxonomy Brucella Meyer and Shaw 1920 Brucella Brucella Meyer and Shaw 1920 GC_ID:11 Brucella melitensis bv. Abortus ncbi_taxonomy Bacterium abortus Brucella melitensis biovar Abortus Brucella abortus Brucella melitensis bv. Abortus Bacterium abortus Brucella melitensis biovar Abortus GC_ID:1 ncbi_taxonomy Cryptosporidium hominis GC_ID:1 ncbi_taxonomy Henipavirus GC_ID:11 PMID:19783615 PMID:8123561 ncbi_taxonomy Francisella GC_ID:11 ncbi_taxonomy Bacterium tularense Brucella tularensis Francisella tularense Pasteurella tularensis Francisella tularensis Bacterium tularense Brucella tularensis Francisella tularense Pasteurella tularensis GC_ID:1 ncbi_taxonomy Metschnikowiaceae Eukaryota Eukaryota GC_ID:1 ncbi_taxonomy Bovinae GC_ID:11 PMID:11541974 PMID:11837318 PMID:16166687 PMID:16403855 PMID:19060069 ncbi_taxonomy Alphabacteria Proteobacteria alpha subdivision Purple bacteria, alpha subdivision a-proteobacteria alpha proteobacteria alpha subdivision alpha subgroup Alphaproteobacteria Alphabacteria Proteobacteria alpha subdivision Purple bacteria, alpha subdivision a-proteobacteria alpha proteobacteria alpha subdivision alpha subgroup Mirela L Vasconcelos Proteobacteria beta subdivision Purple bacteria, beta subdivision beta proteobacteria beta subdivision beta subgroup Betaproteobacteria PEDV Porcine epidemic diarrhea virus NCBITaxon:1435366 NCBITaxon:1435368 NCBITaxon:1435988 NCBITaxon:1439853 NCBITaxon:1487954 NCBITaxon:1487955 GC_ID:11 PMID:12734250 PMID:1283774 ncbi_taxonomy Bacillus pseudomallei Bacterium whitmori Burkholderia pseudomallai Burkholderia pseudomallei MSHR4009 Burkholderia pseudomallei MSHR4018 Burkholderia pseudomallei MSHR44 Burkholderia pseudomallei MSHR7839 Burkholderia sp. MSHR7839 Loefflerella pseudomallei Malleomyces pseudomallei Pseudomonas pseudomallei Burkholderia pseudomallei Bacillus pseudomallei Bacterium whitmori Burkholderia pseudomallai Burkholderia pseudomallei MSHR4009 Burkholderia pseudomallei MSHR4018 Burkholderia pseudomallei MSHR44 Burkholderia pseudomallei MSHR7839 Burkholderia sp. MSHR7839 Loefflerella pseudomallei Malleomyces pseudomallei Pseudomonas pseudomallei Mirela L Vasconcelos Bacillus cholerae-suis Salmonella cholerae-suis Salmonella choleraesuis Salmonella enterica ser. choleraesuis Salmonella enterica GC_ID:1 ncbi_taxonomy Hepeviridae GC_ID:1 ncbi_taxonomy Ancylostoma GC_ID:1 dog hookworm ncbi_taxonomy Ancylostoma caninum dog hookworm GC_ID:1 ncbi_taxonomy Tick-borne encephalitis viruses tick-borne encephalitis virus group Tick-borne encephalitis viruses GC_ID:11 PMID:8573514 ncbi_taxonomy Micrococcus melitensis Streptococcus Miletensis Brucella melitensis Micrococcus melitensis Streptococcus Miletensis GC_ID:11 Brucella melitensis bv. Suis ncbi_taxonomy Brucella melitensis biovar Suis Brucella suis Brucella melitensis bv. Suis Brucella melitensis biovar Suis Mirela L Vasconcelos Proteobacteria epsilon subdivision Purple bacteria, epsilon subdivision epsilon proteobacteria epsilon subdivision epsilon subgroup not Epsilobacteria Epsilonproteobacteria Spondweni virus group Spondweni virus group Mirela L Vasconcelos Schistosomatoidea Mirela L Vasconcelos blood flukes Schistosomatidae GC_ID:1 PMID:11214318 PMID:11214319 PMID:12878460 ncbi_taxonomy Laurasiatheria Euarchontoglires Anthropoidea Simiiformes Cercopithecoidea CV-A16 CVA-16 CVA16 GC_ID:1 ncbi_taxonomy Coxsackie A virus type 16 Human coxsackievirus A16 Human enterovirus CVA16 Coxsackievirus A16 CV-A16 CVA-16 CVA16 Coxsackie A virus type 16 Human coxsackievirus A16 Human enterovirus CVA16 GC_ID:1 higher plants land plants plants ncbi_taxonomy land plants Embryophyta higher plants land plants plants land plants GC_ID:11 ncbi_taxonomy Clostridiaceae GC_ID:11 PMID:10555347 PMID:1283774 PMID:25566316 ncbi_taxonomy Pseudomonas RNA homology group II Burkholderia Pseudomonas RNA homology group II tetrapods Tetrapoda amniotes GC_ID:1 amniotes ncbi_taxonomy Amniota Amniota amniotes authority: Theria Parker & Haswell, 1897 Theria GC_ID:1 diapsids ncbi_taxonomy Diapsida Sauria diapsids Diapsida Orthoretrovirinae H5N6 subtype of Influenza A virus H5N6 subtype GC_ID:1 ncbi_taxonomy Entamoebida Entamoebidae Entamoebida GC_ID:1 green plants ncbi_taxonomy Chlorobionta Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants Viridiplantae green plants Chlorobionta Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants GC_ID:1 ncbi_taxonomy Fungi/Metazoa group opisthokonts Opisthokonta Opisthokonta Fungi/Metazoa group opisthokonts NCBITaxon:259362 NCBITaxon:36053 NCBITaxon:5102 GC_ID:1 PMID:17486980 ncbi_taxonomy Gymnoascales Onygenales Gymnoascales Metazoa Bilateria GC_ID:1 hookworms ncbi_taxonomy Ancylostomatoidea hookworms GC_ID:1 ncbi_taxonomy Ancylostomatidae Protostomia H7N9 subtype of Influenza A virus H7N9 subtype Neoptera Endopterygota deuterostomes Deuterostomia GC_ID:1 carnivores ncbi_taxonomy carnivores Carnivora carnivores carnivores Matthew Diller William R. Hogan alveolates Alveolata Mirela L Vasconcelos Euglenozoans Euglenozoa GC_ID:11 PMID:11760958 PMID:8240958 ncbi_taxonomy Rickettsieae Philip 1957 (Approved Lists 1980) emend. Brenner et al. 1993 Rickettsieae Rickettsieae Philip 1957 (Approved Lists 1980) emend. Brenner et al. 1993 GC_ID:11 PMID:16280474 PMID:22939414 PMID:26747442 ncbi_taxonomy Francisella group Francisellaceae Francisella group GC_ID:1 ncbi_taxonomy Cryptosporidae Cryptosporiidae Cryptosporidiidae Cryptosporidae Cryptosporiidae GC_ID:1 ncbi_taxonomy dsDNA virus, no RNA stage dsDNA viruses, no RNA stage Retroid viruses Retro-transcribing viruses ssRNA positive-strand viruses, no DNA stage http://purl.obolibrary.org/obo/obi.owl ssRNA positive-strand viruses, no DNA stage ssRNA negative-strand virus NCBITaxon:35512 GC_ID:1 ncbi_taxonomy California bunyavirus group California encephalitis virus group California serogroup California virus California encephalitis virus California bunyavirus group California encephalitis virus group California serogroup California virus Mirela L Vasconcelos dsRNA nonenveloped viruses dsRNA viruses GC_ID:1 ncbi_taxonomy Streptophyta GC_ID:1 ncbi_taxonomy Artiodactyla Suiformes Suina Artiodactyla Suiformes GC_ID:1 ncbi_taxonomy Pecora GC_ID:1 Equus ncbi_taxonomy Equus subg. Equus Equus <subgenus> Equus Equus subg. Equus GC_ID:1 ncbi_taxonomy Jamestown Canyon virus GC_ID:11 PMID:16403855 PMID:1854635 rhizobacteria ncbi_taxonomy Rhizobiaceae group alpha-2 proteobacteria Rhizobiales rhizobacteria Rhizobiaceae group alpha-2 proteobacteria Matthew Diller malaria parasite p. ovale Plasmodium ovale GC_ID:11 ncbi_taxonomy Streptococcus sp. (group A) group A streptococci group A streptococcus Streptococcus sp. 'group A' Streptococcus sp. (group A) group A streptococci group A streptococcus GC_ID:11 Brucella melitensis bv. Canis ncbi_taxonomy Brucella melitensis biovar Canis Brucella canis Brucella melitensis bv. Canis Brucella melitensis biovar Canis GC_ID:1 ncbi_taxonomy Clavispora Chikungunya virus Haplorrhini GC_ID:1 ncbi_taxonomy Caniformia EV-71 EV-A71 EV71 GC_ID:1 ncbi_taxonomy Enterovirus 71 Enterovirus EV-A71 Human enterovirus 71 Human enterovirus A71 Human enterovirus type 71 enterovirus type 71 Enterovirus A71 EV-71 EV-A71 EV71 Enterovirus 71 Enterovirus EV-A71 Human enterovirus 71 Human enterovirus A71 Human enterovirus type 71 enterovirus type 71 GC_ID:1 ncbi_taxonomy Rubulavirus Mirela L Vasconcelos Deltavirus GC_ID:11 PMID:10555350 ncbi_taxonomy Calymmatobacterium granulomatis Donovania granulomatis Encapsulatus inguinalis Klebsiella granulomatis Calymmatobacterium granulomatis Donovania granulomatis Encapsulatus inguinalis GC_ID:1 ncbi_taxonomy Yellow fever viruses Yellow fever virus group Yellow fever viruses mammals Mammalia Matthew Diller plasmodium Plasmodium (Plasmodium) Matthew Diller laverania Plasmodium (Laverania) Culicoidea Matthew Diller William R. Hogan hematozoa Aconoidasida GC_ID:1 ncbi_taxonomy Eimeriorina Enterovirus D68 GC_ID:1 dinosaur dinosaurs ncbi_taxonomy Dinosauria dinosaur dinosaurs GC_ID:1 ncbi_taxonomy Saurischia GC_ID:1 ncbi_taxonomy Theropoda GC_ID:1 ncbi_taxonomy Coelurosauria Culicomorpha GC_ID:1 ncbi_taxonomy Anophelinae Culicinae ssRNA virus GC_ID:1 ncbi_taxonomy Koutango virus GC_ID:11 PMID:434652 ncbi_taxonomy Legionellaceae Brenner et al. 1979 Legionellaceae Legionellaceae Brenner et al. 1979 GC_ID:1 ncbi_taxonomy Cyclospora GC_ID:1 Anopheles ncbi_taxonomy Anopheles <subgenus> Anopheles NCBITaxon:29550 GC_ID:11 PMID:16166707 PMID:434652 PMID:8573522 PMID:9734026 ncbi_taxonomy Legionella GC_ID:1 PMID:15689432 PMID:16151185 PMID:17010206 PMID:17051209 PMID:17572334 ncbi_taxonomy Dikarya GC_ID:1 ncbi_taxonomy Eurotiomycetidae GTOV GC_ID:1 ncbi_taxonomy Guanarito arenavirus Guanarito virus Guanarito mammarenavirus GTOV Guanarito arenavirus Guanarito virus GC_ID:1 ncbi_taxonomy Inkoo virus GC_ID:1 ncbi_taxonomy Tahyna virus GC_ID:1 ncbi_taxonomy Sabi mammarenavirus Sabia arenavirus Sabia virus Sabio virus Sabia mammarenavirus Sabi mammarenavirus Sabia arenavirus Sabia virus Sabio virus GC_ID:1 ncbi_taxonomy Trichinella britovi Picornavirales GC_ID:1 ncbi_taxonomy Perdicinae GC_ID:1 ncbi_taxonomy Meleagridinae Mirela L Vasconcelos Acinetobacteraceae Branhamaceae Moraxellaceae Mirela L Vasconcelos Acinetobacter Mirela L Vasconcelos Acinetobacter genomosp. 2 Acinetobacter genomospecies 2 Bacterium anitratum Acinetobacter baumannii GC_ID:1 ncbi_taxonomy Sarcoptinae GC_ID:1 PMID:11062127 PMID:12684019 fungi ncbi_taxonomy fungi Fungi fungi fungi Mirela L Vasconcelos Schizotrypanum GC_ID:11 PMID:19019760 PMID:25831531 ncbi_taxonomy Mycobacterium lepromatosis Mirela L Vasconcelos Neisseriaceae Mirela L Vasconcelos "Gonococcus" Lindau 1898 "Merismopedia" Zopf 1885 Gonococcus Neisseria Mirela L Vasconcelos Diplococcus gonorrhoeae Gonococcus neisseri Merismopedia gonorrhoeae Micrococcus der gonorrhoe Micrococcus gonococcus Micrococcus gonorrhoeae Neisseria gonorrhoeae Mirela L Vasconcelos Diplokokkus intracellularis meningitidis Micrococcus intracellularis Micrococcus meningitidis Micrococcus meningitidis cerebrospinalis Neisseria weichselbaumii Neisseria meningitidis GC_ID:1 PMID:17572334 ascomycetes sac fungi ncbi_taxonomy ascomycetes Ascomycota ascomycetes sac fungi ascomycetes GC_ID:1 ncbi_taxonomy Hemiascomycetes Saccharomycetes Hemiascomycetes GC_ID:1 budding yeasts ncbi_taxonomy Endomycetales Saccharomycetales budding yeasts Endomycetales GC_ID:1 ncbi_taxonomy Candida auris Insecta Mirela L Vasconcelos Alcaligenaceae GC_ID:1 ncbi_taxonomy Ancylostoma duodenale Mirela L Vasconcelos Chlamydiales Mirela L Vasconcelos Bordetella GC_ID:1 ncbi_taxonomy Culex pipiens complex Mirela L Vasconcelos Bacterium tussis-convulsivae Hemophilus pertussis Microbe de la coqueluche Bordetella pertussis GC_ID:1 ncbi_taxonomy Sarcoptidae GC_ID:1 ncbi_taxonomy Sarcoptes NCBITaxon:197185 NCBITaxon:198574 NCBITaxon:268761 NCBITaxon:268762 NCBITaxon:268763 NCBITaxon:337908 GC_ID:1 ncbi_taxonomy Sarcoptes scabiei type canis Sarcoptes scabiei type chimp Sarcoptes scabiei type hominis Sarcoptes scabiei type suis Sarcoptes scabiei type wallaby Sarcoptes scabiei type wombati Sarcoptes scabiei var. canis Sarcoptes scabiei var. chimp Sarcoptes scabiei var. hominis Sarcoptes scabiei var. nyctereutis Sarcoptes scabiei var. suis Sarcoptes scabiei var. wallaby Sarcoptes scabiei var. wombati Sarcoptes scabiei Sarcoptes scabiei type canis Sarcoptes scabiei type chimp Sarcoptes scabiei type hominis Sarcoptes scabiei type suis Sarcoptes scabiei type wallaby Sarcoptes scabiei type wombati Sarcoptes scabiei var. canis Sarcoptes scabiei var. chimp Sarcoptes scabiei var. hominis Sarcoptes scabiei var. nyctereutis Sarcoptes scabiei var. suis Sarcoptes scabiei var. wallaby Sarcoptes scabiei var. wombati GC_ID:1 ncbi_taxonomy Ancylostomatinae GC_ID:1 Culex ncbi_taxonomy Culex <subgenus> Culex Stegomyia GC_ID:1 ncbi_taxonomy Culicini Mirela L Vasconcelos Enterobacteraceae Enterobacteriaceae Mirela L Vasconcelos Bacterium paratyphi Bacterium paratyphi typhus A Salmonella choleraesuis choleraesuis (serotype paratyphi A) Salmonella choleraesuis subsp. choleraesuis serovar Paratyphi A Salmonella paratyphi Salmonella paratyphi A Salmonella paratyphi-a Salmonella enterica subsp. enterica serovar Paratyphi A NCBITaxon:59206 GC_ID:11 PMID:15653929 PMID:15653930 PMID:2915026 PMID:4011990 PMID:7149525 ncbi_taxonomy Salmonella cholerae-suis subsp. bongori Salmonella choleraesuis subsp. bongori Salmonella enterica V Salmonella enterica subsp. V Salmonella enterica subsp. bongori Salmonella bongori Salmonella cholerae-suis subsp. bongori Salmonella choleraesuis subsp. bongori Salmonella enterica V Salmonella enterica subsp. V Salmonella enterica subsp. bongori GC_ID:1 ncbi_taxonomy Herpesvirales GC_ID:1 ncbi_taxonomy Coccidioides GC_ID:1 ncbi_taxonomy Coccidioides immitis GC_ID:1 PMID:23020233 ncbi_taxonomy Amoebozoa GC_ID:1 PMID:23020233 ncbi_taxonomy Archamoebae Mirela L Vasconcelos Escherichia Mirela L Vasconcelos Bacillus coli Bacterium coli Bacterium coli commune E. coli Enterococcus coli Escherichia coli Mirela L Vasconcelos Kinetoplastea Protomonadida kinetoplasts Kinetoplastida Mirela L Vasconcelos Trypanosomatidae Ebolavirus bundibugyo Bundibugyo ebolavirus Mirela L Vasconcelos Trypanosoma Mirela L Vasconcelos Trypanosoma cruzi NCBITaxon:39823 GC_ID:11 PMID:10555350 PMID:11411716 PMID:12635932 ncbi_taxonomy Hyalococcus Klebsiella Hyalococcus GC_ID:1 diplomonads ncbi_taxonomy diplomonads Diplomonadida diplomonads diplomonads GC_ID:6 ncbi_taxonomy Hexamitidae GC_ID:1 ncbi_taxonomy Giardia GC_ID:1 PMID:11432808 PMID:19135417 ncbi_taxonomy Giardia duodenalis Giardia lamblia Lamblia intestinalis Giardia intestinalis Giardia duodenalis Giardia lamblia Lamblia intestinalis GC_ID:1 ncbi_taxonomy Entamoeba Matthew Diller William R. Hogan apicomplexans Apicomplexa GC_ID:1 ncbi_taxonomy coccidians Coccidia coccidians GC_ID:1 ncbi_taxonomy Eimeriids Eimeriidae Eimeriids GC_ID:1 ncbi_taxonomy Cryptosporidium GC_ID:1 ncbi_taxonomy Cryptosporidium parvum Matthew Diller William R. Hogan haemosporidians haemosporina Haemosporida Matthew Diller Plasmodium Matthew Diller Mirela L Vasconcelos malaria parasite P. falciparum plasmodium (laverania) falciparum Plasmodium falciparum Matthew Diller malaria parasite p. vivax Plasmodium vivax Matthew Diller Plasmodium malariae Mirela L Vasconcelos Salmonella Mirela L Vasconcelos Salmonella cholerae-suis subsp. cholerae-suis Salmonella choleraesuis subsp. choleraesuis Salmonella enterica I Salmonella enterica subsp. I Salmonella enterica subsp. enterica Eumetazoa Mirela L Vasconcelos flatworms Platyhelminthes Mirela L Vasconcelos Trematoda Mirela L Vasconcelos flukes Digenea Mirela L Vasconcelos Strigeidida Mirela L Vasconcelos Schistosoma Mirela L Vasconcelos Schistosoma mansoni Mirela L Vasconcelos Schistosoma haematobium GC_ID:11 PMID:26834722 ncbi_taxonomy Shigella GC_ID:11 PMID:12054222 Escherichia/Shigella dysenteriae ncbi_taxonomy Bacillus dysenteriae Bacillus dysentericus Bacillus shigae Eberthella dysenteriae Shigella shigae Shigella dysenteriae Escherichia/Shigella dysenteriae Bacillus dysenteriae Bacillus dysentericus Bacillus shigae Eberthella dysenteriae Shigella shigae GC_ID:11 Escherichia/Shigella flexneri ncbi_taxonomy Shigella paradysenteriae Shigella flexneri Escherichia/Shigella flexneri Shigella paradysenteriae GC_ID:1 nematode nematodes roundworm roundworms ncbi_taxonomy Nemata nematodes Nematoda nematode nematodes roundworm roundworms Nemata nematodes NCBITaxon:33251 GC_ID:1 ncbi_taxonomy Rhabditida GC_ID:11 ncbi_taxonomy Bacterium sonnei Shigella sonnei Bacterium sonnei GC_ID:11 Yersinia ncbi_taxonomy Yersinia <bacteria> Yersinia GC_ID:11 ncbi_taxonomy Bacterium enterocoliticum Yersinia enterocolitica Bacterium enterocoliticum GC_ID:1 ncbi_taxonomy Strongylida GC_ID:11 PMID:15084509 ncbi_taxonomy Bacillus pestis Bacterium pestis Pasteurella pestis Pestisella pestis Yersinia pseudotuberculosis subsp. pestis Yersinia pestis Bacillus pestis Bacterium pestis Pasteurella pestis Pestisella pestis Yersinia pseudotuberculosis subsp. pestis NCBITaxon:36085 NCBITaxon:6331 GC_ID:1 ncbi_taxonomy Trichocephalida GC_ID:1 ncbi_taxonomy Trichinellidae GC_ID:1 ncbi_taxonomy Trichinella GC_ID:1 ncbi_taxonomy Trichinella spiralis GC_ID:1 ncbi_taxonomy Trichinella nativa GC_ID:1 ncbi_taxonomy Trichinella nelsoni Mirela L Vasconcelos Vibrionaceae Zika virus Zika virus GC_ID:1 ncbi_taxonomy Lujo virus Lujo mammarenavirus Lujo virus Mirela L Vasconcelos Beneckea Listonella Microspira Pacinia Vibrio Arthropoda Mirela L Vasconcelos Bacillo virgola del Koch Bacillus cholerae Bacillus cholerae-asiaticae Kommabacillus Liquidivibrio cholerae Microspira comma Pacinia cholerae-asiaticae Spirillum cholerae Spirillum cholerae-asiaticae Vibrio cholera Vibrio cholerae Pacini 1854 Vibrio cholerae-asiaticae Vibrio comma Vibrio cholerae GC_ID:11 PMID:14071901 PMID:4935323 ncbi_taxonomy Beneckea parahaemolytica Oceanomonas parahaemolytica Pasteurella parahaemolytica Vibrio parahemolyticus Vibrio parahaemolyticus Beneckea parahaemolytica Oceanomonas parahaemolytica Pasteurella parahaemolytica Vibrio parahemolyticus GC_ID:11 PMID:1015934 PMID:8186099 ncbi_taxonomy Beneckea vulnifica Vibrio vulnificus Beneckea vulnifica GC_ID:1 chelicerates ncbi_taxonomy Chelicerata chelicerates GC_ID:6 ncbi_taxonomy Giardiinae Mirela L Vasconcelos not Thiobacteria delta/epsilon subdivisions GC_ID:1 arachnids ncbi_taxonomy arachnids Arachnida arachnids arachnids Mirela L Vasconcelos Sedoreovirinae GC_ID:1 mites and ticks ncbi_taxonomy Acarina mites & ticks Acari mites and ticks Acarina mites & ticks Coronavirinae Coronavirus group 1 Group 1 species Alphacoronavirus Betacoronavirus GC_ID:1 ncbi_taxonomy Acariformes NCBITaxon:41437 NCBITaxon:41440 NCBITaxon:41441 GC_ID:1 ncbi_taxonomy Astigmata Hexapoda Mirela L Vasconcelos Pasteurellaceae Diptera Nematocera mosquitos Culicidae Aedes Stegomyia aegypti Aedes aegypti GC_ID:1 Anopheles ncbi_taxonomy Anopheles <genus> Anopheles GC_ID:1 ncbi_taxonomy saccharomyceta GC_ID:1 ncbi_taxonomy leotiomyceta NCBITaxon:44555 GC_ID:1 Culex ncbi_taxonomy Culex <genus> Culex GC_ID:1 PMID:12597651 southern house mosquito ncbi_taxonomy Culex fatigan Culex fatigans Culex pipiens fatigans Culex pipiens quinquefasciatus Culex pipiens quiquefasciatus Culex quinquifasciatus Culex quinquifasiatus Culex quiquefasciatus Culex quinquefasciatus southern house mosquito Culex fatigan Culex fatigans Culex pipiens fatigans Culex pipiens quinquefasciatus Culex pipiens quiquefasciatus Culex quinquifasciatus Culex quinquifasiatus Culex quiquefasciatus GC_ID:11 PMID:17704223 ncbi_taxonomy Vibrio harveyi clade Vibrio harveyi group Vibrio harveyi clade GC_ID:11 PMID:16280474 ncbi_taxonomy Thiomicrospira group Thiothrix/Francisella group Thiotrichales Thiomicrospira group Thiothrix/Francisella group Mirela L Vasconcelos Pseudomonaceae/Moraxellaceae group Pseudomonadales Mirela L Vasconcelos Helicobacter group Helicobacteraceae GC_ID:11 ncbi_taxonomy Campylobacter group Campylobacteraceae Vandamme and De Ley 1991 Campylobacteraceae Campylobacter group Campylobacteraceae Vandamme and De Ley 1991 Mirela L Vasconcelos Haemophilus Mirela L Vasconcelos Bacterium influenzae Coccobacillus pfeifferi Haemophilus meningitidis Influenza-bacillus Mycobacterium influenzae Haemophilus influenzae GC_ID:11 Haemophilus ducreyi ncbi_taxonomy Bacillus ulceris cancrosi Coccobacillus ducreyi [Haemophilus] ducreyi Haemophilus ducreyi Bacillus ulceris cancrosi Coccobacillus ducreyi Pterygota GC_ID:1 ncbi_taxonomy Eucoccidiida Eucoccidiorida Eucoccidiida GC_ID:11 PMID:11760958 PMID:8240958 rickettsias ncbi_taxonomy Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Brenner et al. 1993 Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Dumler et al. 2001 alpha-1 proteobacteria Rickettsiales rickettsias Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Brenner et al. 1993 Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Dumler et al. 2001 alpha-1 proteobacteria GC_ID:11 PMID:11760958 ncbi_taxonomy Anaplasma Theiler 1910 (Approved Lists 1980) emend. Dumler et al. 2001 Anaplasma Anaplasma Theiler 1910 (Approved Lists 1980) emend. Dumler et al. 2001 Nidovirales http://purl.obolibrary.org/obo/obi.owl Nidovirales chordates Chordata vertebrates authority: Vertebrata Cuvier, 1812 Vertebrata GC_ID:11 PMID:11760958 PMID:2592342 PMID:8240958 ncbi_taxonomy Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Brenner et al. 1993 Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Dumler et al. 2001 Rickettsiaceae Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Brenner et al. 1993 Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Dumler et al. 2001 GC_ID:11 Coxiella ncbi_taxonomy Burnetia Coxiella <Bacteria> Coxiella Burnetia Mycobacterium tuberculosis complex GC_ID:11 PMID:9226923 ncbi_taxonomy Coxiella burnetii8 Rickettsia burneti Rickettsia diaporica Coxiella burnetii Coxiella burnetii8 Rickettsia burneti Rickettsia diaporica jawed vertebrates Gnathostomata GC_ID:11 PMID:10939649 PMID:11491333 PMID:9103608 ncbi_taxonomy Rickettsia da Rocha-Lima 1916 Rickettsia Rickettsia da Rocha-Lima 1916 GC_ID:11 PMID:15879256 ncbi_taxonomy Rickettsia prowazekii GC_ID:11 ncbi_taxonomy "Dermacentroxenus rickettsii" Wolbach 1919 Dermacentroxenus rickettsii Rickettsia rickettsii (Wolbach 1919) Brumpt 1922 Rickettsia rickettsii "Dermacentroxenus rickettsii" Wolbach 1919 Dermacentroxenus rickettsii Rickettsia rickettsii (Wolbach 1919) Brumpt 1922 GC_ID:11 ncbi_taxonomy Dermacentroxenus typhi Rickettsia mooseri Rickettsia typhi Dermacentroxenus typhi Rickettsia mooseri Mirela L Vasconcelos Burkholderia/Oxalobacter/Ralstonia group Burkholderiales Mirela L Vasconcelos Chlamydiaceae GC_ID:1 ncbi_taxonomy Guaroa virus Mirela L Vasconcelos Bedsonia Chlamydophila Miyagawanella Rakeia Rickettsiaformis Chlamydia Mirela L Vasconcelos Chlamydozoon trachomatis Rickettsia trachomae Rickettsia trachomatis Chlamydia trachomatis Sarcopterygii GC_ID:1 ncbi_taxonomy Sarcoptiformes GC_ID:1 ncbi_taxonomy Listrophoroidea Psoroptoidea Sarcoptoidea Listrophoroidea Psoroptoidea NCBITaxon:812 GC_ID:11 PMID:10319462 PMID:12807198 PMID:8102247 PMID:8347519 ncbi_taxonomy Chlamydia psitacci Chlamydophila psittaci Chlamydozoon psittaci Ehrlichia psittaci Rickettsia psittaci Rickettsiaformis psittacosis Chlamydia psittaci Chlamydia psitacci Chlamydophila psittaci Chlamydozoon psittaci Ehrlichia psittaci Rickettsia psittaci Rickettsiaformis psittacosis GC_ID:1 sauropsids ncbi_taxonomy Sauropsida sauropsids GC_ID:1 ncbi_taxonomy Archosauria Corynebacterineae Corynebacteriales Dicondylia Bacillus cereus group GC_ID:1 birds ncbi_taxonomy birds Aves birds birds GC_ID:1 ncbi_taxonomy Neognathae GC_ID:1 ncbi_taxonomy Anseriformes GC_ID:1 waterfowl ncbi_taxonomy Anatidae waterfowl GC_ID:1 ncbi_taxonomy Cyclospora cayetanensis Panarthropoda Craniata GC_ID:1 fowls ncbi_taxonomy Galliformes fowls NCBITaxon:9099 GC_ID:1 turkeys ncbi_taxonomy Phasianidae turkeys GC_ID:1 ncbi_taxonomy Gallus GC_ID:1 bantam chicken chickens ncbi_taxonomy Gallus domesticus Gallus gallus domesticus Gallus gallus bantam chicken chickens Gallus domesticus Gallus gallus domesticus Mirela L Vasconcelos Bacillus typhi Bacterium (subgen. Eberthella) typhi Salmonella choleraesuis serovar Typhi Salmonella choleraesuis typhi Salmonella enterica ser. typhi Salmonella enterica serotype Typhi Salmonella enterica serovar Typhi Salmonella typhi Salmonella enterica subsp. enterica serovar Typhi GC_ID:1 ncbi_taxonomy Phasianinae GC_ID:1 ncbi_taxonomy Coturnix Staphylococcaceae Staphylococcus group Staphylococcaceae Mirela L Vasconcelos Acinetobacter calcoaceticus/baumannii complex GC_ID:1 ncbi_taxonomy Meleagris GC_ID:1 common turkey turkey wild turkey ncbi_taxonomy Meleagris gallopavo common turkey turkey wild turkey Mirela L Vasconcelos Bacillus/Lactobacillus/Strptococcus group Firmibacteria Bacilli Mirela L Vasconcelos Enterobacteriaceae and related endosymbionts Enterobacteriaceae group Enterobacteriales Enterobacterales GC_ID:1 whales, hippos, ruminants, pigs, camels etc. ncbi_taxonomy even-toed ungulates Cetartiodactyla whales, hippos, ruminants, pigs, camels etc. even-toed ungulates Placentalia eutherian mammals placental mammals placentals Eutheria GC_ID:1 Japanese quail ncbi_taxonomy Coturnix coturnix Japonicus Coturnix coturnix japanica Coturnix coturnix japonica Coturnix japonica japonica Coturnix japonica Japanese quail Coturnix coturnix Japonicus Coturnix coturnix japanica Coturnix coturnix japonica Coturnix japonica japonica GC_ID:11 PMID:11760958 ncbi_taxonomy Anaplasmataceae Philip 1957 (Approved Lists 1980) emend. Dumler et al. 2001 Ehrlichiae Anaplasmataceae Anaplasmataceae Philip 1957 (Approved Lists 1980) emend. Dumler et al. 2001 Ehrlichiae NCBITaxon:778 GC_ID:11 PMID:11414267 PMID:11760958 ncbi_taxonomy "Ehrlichia (subgen. Cowdria)" Moshkovski 1945 "Kurlovia" Zhdanov 1953 "Nicollea" (in part) Macchiavello 1947 "Nicollea" Macchiavello 1947 "Rickettsia (subgen. Ehrlichia)" Moshkovski 1937 Cowdria Cowdria Moshkovski 1947 Ehrlichia (subgen. Cowdria) Ehrlichia Moshkovski 1945 (Approved Lists 1980) emend. Dumler et al. 2001 Kurlovia Nicollea Rickettsia (subgen. Ehrlichia) possibly "Donatienella" Rousselot 1948 Ehrlichia "Ehrlichia (subgen. Cowdria)" Moshkovski 1945 "Kurlovia" Zhdanov 1953 "Nicollea" (in part) Macchiavello 1947 "Nicollea" Macchiavello 1947 "Rickettsia (subgen. Ehrlichia)" Moshkovski 1937 Cowdria Cowdria Moshkovski 1947 Ehrlichia (subgen. Cowdria) Ehrlichia Moshkovski 1945 (Approved Lists 1980) emend. Dumler et al. 2001 Kurlovia Nicollea Rickettsia (subgen. Ehrlichia) possibly "Donatienella" Rousselot 1948 Primata primate primates Primates GC_ID:11 PMID:11760958 PMID:1757557 ncbi_taxonomy Ehrlichia chaffeensis Anderson et al. 1992 emend. Dumler et al. 2001 Ehrlichia chaffensis Ehrlichia chaffeensis Ehrlichia chaffeensis Anderson et al. 1992 emend. Dumler et al. 2001 Ehrlichia chaffensis NCBITaxon:59888 NCBITaxon:75053 NCBITaxon:75115 NCBITaxon:946 GC_ID:11 PMID:1115421 PMID:11760958 PMID:8195363 agent of human granulocytic ehrlichiosis ncbi_taxonomy Anaplasma phagocytophila Cytoecetes bovis Cytoecetes phagocytophila Ehrlichia equi Ehrlichia phagocytophila Ehrlichia sp. 'HGE agent' HGE agent Rickettsia phagocytophila Rickettsia phagocytophila ovis human granulocytic Ehrlichia Anaplasma phagocytophilum agent of human granulocytic ehrlichiosis Anaplasma phagocytophila Cytoecetes bovis Cytoecetes phagocytophila Ehrlichia equi Ehrlichia phagocytophila Ehrlichia sp. 'HGE agent' HGE agent Rickettsia phagocytophila Rickettsia phagocytophila ovis human granulocytic Ehrlichia Catarrhini Old World monkeys monkey monkeys Cercopithecidae Cercopithecinae macaque macaques Macaca NCBITaxon:36519 GC_ID:1 crab eating macaque crab-eating macaque cynomolgus monkey cynomolgus monkeys long-tailed macaque ncbi_taxonomy Macaca cynomolgus Macaca irus cynomolgus macaque Macaca fascicularis crab eating macaque crab-eating macaque cynomolgus monkey cynomolgus monkeys long-tailed macaque Macaca cynomolgus Macaca irus cynomolgus macaque Rhesus monkey rhesus macaque rhesus macaques rhesus monkeys Macaca mulatta Homo sapiens human being Homo sapiens Homo sapiens GC_ID:1 dog, coyote, wolf, fox ncbi_taxonomy Canidae dog, coyote, wolf, fox GC_ID:1 ncbi_taxonomy Canis GC_ID:1 gray wolf grey wolf ncbi_taxonomy Canis lupus gray wolf grey wolf GC_ID:1 dog dogs ncbi_taxonomy Canis canis Canis domesticus Canis familiaris Canis lupus familiaris dog dogs Canis canis Canis domesticus Canis familiaris GC_ID:1 odd-toed ungulates ncbi_taxonomy odd-toed ungulates Perissodactyla odd-toed ungulates odd-toed ungulates GC_ID:1 horses ncbi_taxonomy Equidae horses GC_ID:1 ncbi_taxonomy Equus GC_ID:1 domestic horse equine horse ncbi_taxonomy Equus ferus caballus Equus przewalskii f. caballus Equus przewalskii forma caballus Equus caballus domestic horse equine horse Equus ferus caballus Equus przewalskii f. caballus Equus przewalskii forma caballus NCBITaxon:39423 GC_ID:1 boars pigs ncbi_taxonomy Suidae boars pigs GC_ID:1 ncbi_taxonomy Sus GC_ID:1 pig pigs swine wild boar ncbi_taxonomy Sus scrofus Sus scrofa pig pigs swine wild boar Sus scrofus GC_ID:1 ncbi_taxonomy Artiodactyla Ruminantia Artiodactyla GC_ID:1 ncbi_taxonomy Bovidae GC_ID:1 oxen, cattle ncbi_taxonomy Bos oxen, cattle NCBITaxon:272461 GC_ID:1 bovine cattle cow domestic cattle domestic cow ncbi_taxonomy Bos Tauurus Bos bovis Bos primigenius taurus Bos taurus bovine cattle cow domestic cattle domestic cow Bos Tauurus Bos bovis Bos primigenius taurus GC_ID:1 ncbi_taxonomy Capra NCBITaxon:57076 GC_ID:1 domestic goat goat goats ncbi_taxonomy Capra aegagrus hircus Carpa hircus South African angora goat Capra hircus domestic goat goat goats Capra aegagrus hircus Carpa hircus South African angora goat GC_ID:1 ncbi_taxonomy Ovis NCBITaxon:9936 GC_ID:1 domestic sheep lambs sheep wild sheep ncbi_taxonomy Ovis ammon aries Ovis orientalis aries Ovis ovis Ovis aries domestic sheep lambs sheep wild sheep Ovis ammon aries Ovis orientalis aries Ovis ovis GC_ID:1 ncbi_taxonomy Caprinae A contraindication is a disposition that increases the risk of harm involved in using a particular drug, carrying out a medical procedure, or engaging in a particular activity such that the risk of harm exceeds a threshold. An contraindication serves as a reason to withhold a certain medical treatment. http://en.wikipedia.org/wiki/Contraindication http://purl.obolibrary.org/obo/dideo/dev/dideo.owl contraindication planned process planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 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) planned process processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). investigation 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. 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 http://purl.obolibrary.org/obo/obi.owl intervention design data encoding storage of measurement results from an assay into a text file, such as a documenting process to encode an information entity into a digital document PlanAndPlannedProcess Branch OBI branch derived We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE http://purl.obolibrary.org/obo/obi.owl data encoding 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. An organization is a continuant entity which can play 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 averaging objective A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi http://purl.obolibrary.org/obo/obi.owl averaging objective study design execution a planned process that carries out a study design study design execution scattered molecular aggregate the sodium and chloride ions in a glass of salt water a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates PERSON: Alan Ruttenberg Collective Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 http://purl.obolibrary.org/obo/obi.owl scattered molecular aggregate data representational model gene regulatory graph model phylogenetic tree protein interaction network Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax. Melanie Courtot data structure data structure specification GROUP: OBI 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009 http://purl.obolibrary.org/obo/obi.owl data representational model center value A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. PERSON: James Malone PERSON: Monnie McGee median http://purl.obolibrary.org/obo/obi.owl median center value average value A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. PERSON: James Malone PERSON: Monnie McGee arithmetic mean false http://purl.obolibrary.org/obo/obi.owl A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. mean average value graph of vertices For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities. A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix. Bjoern Peters Chris Stoeckert James Malone WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html http://purl.obolibrary.org/obo/obi.owl graph of vertices 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 device is a processed material which is designed to perform some function or functions 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. food should not classify as a device - counter example for using manufacturer and not device. macroscopic only if we keep this exploratory term we could reinstate the old device class which is obsolete_device. didn't work before as we had manufacturing as part of the definition. device was needed, but couldn't define in Philadelphia. If we decide that in addition to function there are also capabilities for which a device is created we will include these in the definition. PERSON: Helen Parkinson instrument OBI Vancouver workshop 2010 OBI development call 2012-12-17. would include reagents device computer cluster A group of linked computers, working together closely so that in many respects they form a single computer. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Cluster_(computing) http://purl.obolibrary.org/obo/obi.owl computer cluster service providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. Carlo; Matt OBI workshop San Diego 2011 http://purl.obolibrary.org/obo/obi.owl service environmental history design A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc. Person: Chris Stoeckert, Jie Zheng MO_698 environmental_history_design http://purl.obolibrary.org/obo/obi.owl environmental history design disease state design A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress. Person: Chris Stoeckert, Jie Zheng MO_902 disease_state_design http://purl.obolibrary.org/obo/obi.owl disease state design pathogenicity design A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed. Person: Chris Stoeckert, Jie Zheng MO_807 pathogenicity_design http://purl.obolibrary.org/obo/obi.owl pathogenicity design data service Data analysis service such statistical abalysis or storage service such data backup. A service that has some information content entity as input and output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai http://purl.obolibrary.org/obo/obi.owl Information content entity was used as specified input and output since it was more appropriate then data item or dataset. data service rate measurement datum The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time. A scalar measurement datum that represents the number of events occuring over a time interval PERSON: Bjoern Peters, Randi Vita IEDB http://purl.obolibrary.org/obo/obi.owl rate measurement datum investigation description A textual entity that describes an investigation. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group http://purl.obolibrary.org/obo/obi.owl study description project description investigationDescription NIAID GSCID-BRC investigation description latitude coordinate measurement datum A measurement datum that is the measure of the latitude coordinate of a site. Person: Chris Stoeckert, Jie Zheng latitude NIAID GSCID-BRC metadata working group http://purl.obolibrary.org/obo/obi.owl Specimen Collection Location - Latitude NIAID GSCID-BRC latitude coordinate measurement datum longitude coordinate measurement datum A measurement datum that is the measure of the longitude coordinate of a site. Person: Chris Stoeckert, Jie Zheng longitude NIAID GSCID-BRC metadata working group http://purl.obolibrary.org/obo/obi.owl Specimen Collection Location - Longitude NIAID GSCID-BRC longitude coordinate measurement datum investigation identifier A CRID symbol used to identify an investigation. Person: Chris Stoeckert, Jie Zhneg NIAID GSCID-BRC metadata working group http://purl.obolibrary.org/obo/obi.owl project ID investigationLabel NIAID GSCID-BRC investigation identifier grant identifier A CRID symbol used to identify a grant. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group http://purl.obolibrary.org/obo/obi.owl grant ID NIAID GSCID-BRC grant identifier scalar value specification A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters http://purl.obolibrary.org/obo/obi.owl scalar value specification 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 http://purl.obolibrary.org/obo/obi.owl value specification systematic review study design Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/ar\ ticles/PMC4090399/ The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic re\ view. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/ A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according \ to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were no\ t justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed. PERSON: Bill Hogan systematic review study design digital object identifier The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073 A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles. Discussed on Aug 22, 2016 OBI dev call. Details see tracker: https://sourceforge.net/p/obi/obi-terms/818/ OBI developers DOI https://en.wikipedia.org/wiki/Digital_object_identifier https://www.doi.org/ http://purl.obolibrary.org/obo/obi.owl digital object identifier organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism Individual organism data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A data transformation is a process which produces output data from input data A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors http://purl.obolibrary.org/obo/obi.owl data transformation data transformation objective normalize objective A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed. James Malone PERSON: James Malone http://purl.obolibrary.org/obo/obi.owl data transformation objective averaging data transformation An averaging data transformation is a data transformation that has objective averaging. James Malone PERSON: James Malone http://purl.obolibrary.org/obo/obi.owl averaging data transformation 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 http://purl.obolibrary.org/obo/obi.owl observation design predicted data item A data item that was generated on the basis of a calculation or logical reasoning BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted. Philippe Rocca-Serra; Bjoern Peters http://purl.obolibrary.org/obo/obi.owl APOLLO DEVELOPERS: We need to check whether OBI changes the label and the hierarchical place of this class. calculated datum predicted data item digital curation PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44. Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally. Philippe Rocca-Serra wikipedia http://purl.obolibrary.org/obo/obi.owl digital curation computer Apple PowerBook, Dell OptiPlex A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. Melanie Courtot Trish Whetzel http://en.wikipedia.org/wiki/Computer computer 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. http://purl.obolibrary.org/obo/obi.owl study design time series design PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources. Groups of assays that are related as part of a time series. Philippe Rocca-Serra on behalf of MO MO_887 http://purl.obolibrary.org/obo/obi.owl time series design A planned process that realizes the concretization of a software. ITPPR operation ITPPR http://purl.obolibrary.org/obo/OBIws.owl software execution A software execution that is provided by the web service, and involves invoking software execution over network. ITPPR web service operation ITPPR http://purl.obolibrary.org/obo/OBIws.owl web service execution 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 http://purl.obolibrary.org/obo/ogms.owl clinical finding A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:21:58Z http://purl.obolibrary.org/obo/ogms.owl result laboratory finding A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T11:13:49Z http://purl.obolibrary.org/obo/ogms.owl phenotype A clinically abnormal phenotype. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:18:05Z http://purl.obolibrary.org/obo/ogms.owl clinical phenotype 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 disease A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning. Albert Goldfain Barry Smith Richard H. Scheuermann Werner Ceusters Scheuermann RH, Ceusters W, Smith B. Toward an ontological treatment of disease and diagnosis. Summit on translational bioinformatics. 2009;2009:116. Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ creation date: 2009-06-23T11:22:01Z http://purl.obolibrary.org/obo/ogms.owl homeostasis A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:39:44Z http://purl.obolibrary.org/obo/ogms.owl disorder A process in which at least one bodily component of an organsim participates. http://www.jbiomedsem.com/content/1/1/10 From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060 bodily process disease course The totality of all processes through which a given disease instance is realized. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:55:44Z http://purl.obolibrary.org/obo/ido.owl http://purl.obolibrary.org/obo/ogms.owl disease course An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=3 creation date: 2010-01-25T04:51:11Z http://purl.obolibrary.org/obo/ogms.owl From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087 extended organism A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T04:51:11Z http://purl.obolibrary.org/obo/ogms.owl Treatment Apollo-SV currently defines two subclasses of treatment. See vaccination and antiviral treatment. treatment A processual entity which has as parts all the processes in which a given organism is participant. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=38 creation date: 2010-03-31T04:51:11Z http://purl.obolibrary.org/obo/ogms.owl A processual entity which has as parts all the processes in which a given organism is participant. LifeCycle life course A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z http://purl.obolibrary.org/obo/ogms.owl health care process A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z http://purl.obolibrary.org/obo/ogms.owl health care encounter Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z http://purl.obolibrary.org/obo/ogms.owl hospitalization hospitalization Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z http://purl.obolibrary.org/obo/ogms.owl outpatient encounter A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night. Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z http://purl.obolibrary.org/obo/ogms.owl inpatient encounter Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z http://purl.obolibrary.org/obo/ogms.owl ED encounter A part of a disease course that occurs after an incomplete remission and that is similar to earlier parts of the disease course. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=73 http://purl.obolibrary.org/obo/ogms.owl relapse A CRID that constitutes a reference to an Internet resource. Mathias Brochhausen uri http://en.wikipedia.org/wiki/Uniform_resource_locator http://purl.obolibrary.org/obo/omiabis.owl url unique resource locator A social role inhering in a human being. Mathias Brochhausen William R. Hogan human social role A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. Mathias Brochhausen William R. Hogan health care role human health care role A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter. Amanda Hicks Mathias Brochhausen patient CAFE domain expert working group. In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications. patient role A role that inheres in an organization and that is realized by the providing of services in a health care encounter. Mathias Brochhausen Amanda Hicks health care provider organization role An object aggregate of objectual organisms. Any arbitrary collection of organisms. They need not be of the same taxonomic class. aggregate of objectual organisms An object aggregate all of whose components are human beings. collection of humans A role in human social processes that inheres in an organization. William R. Hogan Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants. organization social role A role in human social processes that inheres in an organism. William R. Hogan Mathias Brochhausen Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants. Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc. Previous definition: A role in human social processes played by an organism. organism social role An organization social role that, if realized, is realized by either a health care process or an ancillary health care process Previous definition: An organization social role played by an organization in health care processes. organization health care role A patient role that inheres in a human being. human patient role 2 An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common William R. Hogan Amanda Hicks It is often convenient to group organizations together that otherwise might not even interact with one another. aggregate of organizations material entity role organism role Homo sapiens role organization role A function inhering in a material entity that, if realized, is realized by that material entity being the site at which formal education is provided to a student population. Mathias Brochhausen school function A healthcare provider role that inheres in an organization and is realized by providing inpatient care. Mathias Brochhausen hospital role An organization social role that inheres in an organization and is realized by providing formal education to students. Mathias Brochhausen school role An organization that is the bearer of a hospital role. Mathias Brochhausen hospital organization An organization that is the bearer of a school role. Mathias Brochhausen school organization A human social role that, if realized, is realized by the process of formal education that the bearer undergoes. Mathias Brochhausen student role Mathias Brochhausen nursery school role Mathias Brochhausen primary school role A material entity that is a human made strcuture with firm connection between its foundation and the ground. Mathias Brochhausen http://de.wikipedia.org/wiki/Bauwerk "Building" is a subclass of this. This type of entity is referred to as "Bauwerk" or "Bauliche Anlage". architectural structure An architectural structure that bears some function. Mathias Brochhausen facility 09/09/2017 A facility that is run by a school organization and is the bearer of a school function. Mathias Brochhausen school facility Mathias Brochhausen secondary school role A human social role that is created by a deontic declaration performed by an organization. Amanda Hicks human organizational role human role within an organization An information content entity that is about human travel. https://github.com/ufbmi/OMRSE/issues/79 Jie Zheng Amanda Hicks human traveling information health care function A role that inheres in some entity that is realized in a social act. Matthew Diller Mathias Brochhausen Previous definition: A role played by an entity in human social processes. role in human social processes A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATO:0000001 quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG A quality that is the extent of space between two entities. http://purl.obolibrary.org/obo/pato.owl Distance quality PATO:0000040 distance biological sex 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. http://purl.obolibrary.org/obo/obi.owl biologicalSex biological sex morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. http://purl.obolibrary.org/obo/pato.owl quality PATO:0000051 morphology A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. http://purl.obolibrary.org/obo/pato.owl quality PATO:0000117 size length A 1-D extent quality which is equal to the distance between two points. length mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. mass A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. http://purl.obolibrary.org/obo/pato.owl PATO:0001452 conformation relational structural quality quality PATO:0000141 structure A physical quality of the thermal energy of a system. http://purl.obolibrary.org/obo/pato.owl quality PATO:0000146 temperature female A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. http://purl.obolibrary.org/obo/obi.owl female male A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. http://purl.obolibrary.org/obo/obi.owl male physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. http://purl.obolibrary.org/obo/pato.owl PATO:0002079 Wikipedia:Physical_property relational physical quality quality PATO:0001018 physical quality physical object quality A quality which inheres in a continuant. http://purl.obolibrary.org/obo/pato.owl 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 A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent. http://purl.obolibrary.org/obo/pato.owl quality PATO:0001323 MIREOT'd into GEO to represent the area quality of a geographical region, including land area and water area. area A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. http://purl.obolibrary.org/obo/pato.owl 1-D size quality PATO:0001708 1-D extent A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions. http://purl.obolibrary.org/obo/pato.owl 2-D size quality PATO:0001709 2-D extent A structural quality inhering in a bearer by virtue of the bearer's touching another entity. http://purl.obolibrary.org/obo/pato.owl quality contiguous PATO:0001961 in contact with A length quality which is equal to the length of any straight line segment that passes from the center of a circle to any endpoint on the circular boundary. The radius is half of the diameter. http://purl.obolibrary.org/obo/pato.owl radius gkoutos 2012-11-15T05:17:15Z quality PATO:0002390 radius Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. A material entity that consists of two or more organisms, viruses, or viroids. group of organisms organism collection May be of the same or different species. PCO:collection of organisms A collection of organisms, all of the same species, that live in the same place. Still uncertain if this should include every organism of a species living in an area or any subset of them. For now make this a general term (unspecified) and then subclasses can be more specific. ISBN:0878932739 Population It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across ontologies and only one term used. population A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. collection of organisms of the same species http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/ effect size estimate is a data item about the direction and strength of the consequences of a causative agent as explored by statistical methods. Those methods produce estimates of the effect size, e.g. confidence interval Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra AGB,PRS http://purl.obolibrary.org/obo/stato.owl effect size effect size estimate statistical sample size is a count evaluating the number of individual experimental units Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra AGB-PRS http://purl.obolibrary.org/obo/stato.owl statistical sample size sampleSize study group population size specificity is a measurement datum qualifying a binary classification test and is computed by substracting the false positive rate to the integral numeral 1 Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra specificity true negative rate sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1 Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra recall sensitivity adapted from: http://en.wikipedia.org/wiki/Sensitivity_and_specificity and http://mathworld.wolfram.com/Sensitivity.html true positive rate Relative risk is a measurement datum which denotes the risk of an 'event' relative to an 'exposure'. Relative risk is calculated by forming the ratio of the probability of the event occurring in the exposed group versus the probability of this event occurring in the non-exposed group. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra risk ratio http://purl.obolibrary.org/obo/stato.owl relative risk a categorical variable is a variable which that can only assume a finite number of value and cast observation in a small number of categories Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra discrete variable nominal variable qualitative factor http://udel.edu/~mcdonald/statvartypes.html http://purl.obolibrary.org/obo/stato.owl categoricalVariable https://onlinecourses.science.psu.edu/stat503/node/7 categorical variable a variable is a data item which can assume any of a set of values, either as determined by an agent or as randomly occuring through observation. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra STATO adapted from wolfram-alpha (http://www.wolframalpha.com/input/?i=variable) definition 2. and from Oxford English Dictionary: http://www.oed.com/view/Entry/221514?redirectedFrom=variable#eid, definition B,1 http://purl.obolibrary.org/obo/stato.owl variable variable Probability distribution estimated empirically on the data without assumptions on the shape of the probability distribution. Camille Maumet Karl Helmer Philippe Rocca-Serra Thomas Nichols http://purl.obolibrary.org/obo/stato.owl NonparametricProbabilityDistribution Initially discussed at https://github.com/incf-nidash/nidm/pull/191 non-parametric distribution The weighted arithmetic mean is a measure of central tendency that is the sum of the products of each observed value and their respective non-negative weights, divided by the sum of the weights, such that the contribution of each observed value to the mean may defer according to its respective weight. It is defined by the formula: A = sum(vi*wi)/sum(wi), where 'i' ranges from 1 to n, 'vi' is the value of each observation, and 'wi' is the value of the respective weight for each observed value. The weighted arithmetic mean is a kind of mean similar to an ordinary arithmetic mean (the most common type of average), except that instead of each of the data points contributing equally to the final average, some data points are weighted, meaning they contribute more than others. The weighted arithmetic mean is often used if one wants to combine average values from samples of the same population with different sample sizes. Alejandra Gonzalez-Beltran Matthew Diller Orlaith Burke Philippe Rocca-Serra https://en.wikipedia.org/wiki/Weighted_arithmetic_mean https://docs.scipy.org/doc/numpy/reference/generated/numpy.average.html np.average(range(1,11), weights=range(10,0,-1)) https://github.com/ISA-tools/stato/issues/59 weighted arithmetic mean A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species. Suggested label: pathogen transmission process Transmission Ontology: http://purl.obolibrary.org/obo/trans.owl transmission process Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome. Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. http://purl.obolibrary.org/obo/uberon.owl AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:A13 MESH:D000825 SCTID:362889002 TAO:0000037 TGMA:0001823 VHOG:0001759 WBbt:0000100 XAO:0003000 ZFA:0000037 http://dbpedia.org/ontology/AnatomicalStructure biological structure connected biological structure uberon UBERON:0000061 anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 connected biological structure CARO:0000003 Anatomical entity that has mass. http://purl.obolibrary.org/obo/uberon.owl AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 uberon UBERON:0000465 material anatomical entity Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]. http://purl.obolibrary.org/obo/uberon.owl Anatomical group that has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[TAO] Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[AAO] Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[CARO] system AAO:0000007 AEO:0000011 BILA:0000011 BSA:0000049 CALOHA:TS-2088 CARO:0000011 EHDAA2:0003011 EHDAA:392 EMAPA:16103 EV:0100000 FBbt:00004856 FMA:7149 HAO:0000011 MA:0000003 NIF_GrossAnatomy:birnlex_14 OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ SCTID:278195005 TAO:0001439 TGMA:0001831 UMLS:C0460002 VHOG:0001725 WBbt:0005746 WBbt:0005763 Wikipedia:Organ_system XAO:0003002 ZFA:0001439 galen:AnatomicalSystem ncithesaurus:Organ_System body system organ system uberon UBERON:0000467 anatomical system Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. http://purl.obolibrary.org/obo/uberon.owl AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:A10 NIF_GrossAnatomy:birnlex_19 TAO:0001477 TGMA:0001844 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 galen:Tissue ncithesaurus:Tissue portion of tissue tissue portion simple tissue uberon UBERON:0000479 Editor note: changed label and definition to reflect CARO2 tissue Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue. http://purl.obolibrary.org/obo/uberon.owl AAO:0010008 AEO:0000054 BILA:0000054 CARO:0000054 EHDAA2:0003054 HAO:0000054 TAO:0001512 TGMA:0001846 VHOG:0001724 XAO:0003001 ZFA:0001512 uberon UBERON:0000480 anatomical group Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. AAO:0010841 AEO:0000000 BFO:0000004 BILA:0000000 BIRNLEX:6 CARO:0000000 EHDAA2:0002229 FMA:62955 HAO:0000000 MA:0000001 NCIT:C12219 TAO:0100000 TGMA:0001822 UMLS:C1515976 WBbt:0000100 XAO:0000000 ZFA:0100000 UBERON:0001062 anatomical entity Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. FMA:62955 http://orcid.org/0000-0001-9114-8737 UMLS:C1515976 ncithesaurus:Anatomic_Structure_System_or_Substance Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. http://purl.obolibrary.org/obo/uberon.owl The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] AAO:0011003 BILA:0000104 FMA:9825 GAID:328 MA:0002711 MESH:A15.382 OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA SCTID:362590003 TAO:0001159 UMLS:C0020962 VHOG:0001247 Wikipedia:Immune_system XAO:0003152 ZFA:0001159 ncithesaurus:Immune_System uberon UBERON:0002405 This class was created automatically from a combination of ontologies immune system An anatomical structure that has more than one cell as a part. http://purl.obolibrary.org/obo/uberon.owl CARO:0010000 FBbt:00100313 multicellular structure uberon UBERON:0010000 multicellular anatomical structure An anatomical structure that has more than one cell as a part. CARO:0010000 multicellular structure FBbt:00100313 A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity. http://purl.obolibrary.org/obo/uberon.owl uberon UBERON:0035943 life cycle temporal boundary A life cycle temporal boundary that marks the end of the life cycle of the organism. http://purl.obolibrary.org/obo/uberon.owl end of life cycle moment of death time of death uberon death end of life UBERON:0035944 life-death temporal boundary http://purl.org/obo/owl/unit unit.ontology unit length unit length unit mass unit mass unit time unit unitOfTime time unit A unit which is a standard measure of the amount of a 2-dimensional flat surface. http://purl.obolibrary.org/obo/uo.owl george gkoutos unit.ontology UO:0000047 area unit A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. http://purl.org/obo/owl/unit DimensionlessUnit unit.ontology dimensionless unit A dimensionless ratio unit which denotes numbers as fractions of 100. http://purl.org/obo/owl/unit Percent unit.ontology percent A dimensionless unit which denotes an amount or magnitude of one quantity relative to another. http://purl.org/obo/owl/unit Ratio unit.ontology ratio A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator). http://purl.org/obo/owl/unit Fraction unit.ontology fraction A unit which represents a standard measurement occurrence of a process per unit time. http://purl.org/obo/owl/unit Rate unit.ontology rate unit A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine. Many vaccines are developed to protect against infectious pathogens. Many vaccines are also being developed against some diseases such as cancer and autoimmune diseases. Vaccine is developed against a disease. Allergy. YH, BP, BS, MC, LC, XZ, RS a role that inheres in a prepared material entity that is designed to induce protection or treament for a diease or infection in vivo. http://purl.obolibrary.org/obo/vo.owl Vaccine vaccine MeSH: D014612 A vaccine contraindication is a contraindication that increases the risks of a vaccination. YH contraindication for vaccination http://purl.obolibrary.org/obo/vo.owl VaccineContraindications vaccine contraindication vaccine function is a function that inheres in a vaccine that induces protective immune response against a disease. It is realized in the immunization process in the host. PERSPN: Oliver He: There has been hot discussion about whether we use 'vaccine function' or 'vaccine role'. Vaccine role may not be the good term to use. Vaccine is designed to be 'vaccine', so it should be vaccine function. One special case is cowpox virus. The cowpox virus can be mixed with some liquid like water and used as a smallpox vaccine. In this case, people often say: the cowpox virus has a 'vaccine role'. However, the cowpox virus vaccine is a processed material of a mix of the virus with water. The virus is a virus, it is not a vaccine per se. Therefore, vaccine role may not be an accurate term. YH, MC, XZ, and AR http://purl.obolibrary.org/obo/vo.owl vaccine function vaccine preparation is a manufacturing process to produce a vaccine. YH, BP vaccine generation vaccine production http://purl.obolibrary.org/obo/vo.owl vaccine preparation The specificity of a system that classifies organisms into the binary categories of individual who meets the criteria of a particular case definition and individual who does NOT meet the criteria of a particular type of disease X. William R. Hogan The specificity of a process or system that detects organisms who satisfy a case definition. specificityOfCaseDetection deprecated due to malformed URI and created anew. obsolete specificity of case detection true the specificity of a system that classifies organisms into the binary categories of having received a particular treatment and not having received a particular treatment William R. Hogan the specificity of the process or system that detects organisms that have undergone a particular treatment specificityOfTreatmentDetection Deprecated due to malformed URI and created anew. obsolete specificity of treatment detection true the sensitivity of a system that classifies organisms into the binary categories of having received a particular treatment and not having received a particular treatment William R. Hogan the sensitivity of the process or system that detects organisms that have undergone a particular treatment sensitivityOfTreatmentDetection Deprecated due to malformed URI and created anew. obsolete sensitivity of treatment detection true Amanda Hicks e.g., the EU supranational entity http://purl.org/obo/owl/flybase_vocab pub_type Originally imported into Apollo-SV for purpose of indexing in OBC.ide news articles relevant to infectious disease epidemiology. news article Genomic data is data about the genomes of an organism. James Malone genomic data http://www.geneontology.org/formats/oboInOwl Obsolete Class Obsolete Class obsolete_class organism population universal atmosphere of the Earth angular degree angular degree ° radian A unit of measurement of planar angles where a full circle is 2π. Specifically the angle is the length of the arc subtended by the angle divided by the circumference of the circle. Josh Hanna William R. Hogan Technically in the S.I. system it is a derived unit m•m^-1. rad radian square mile An area unit which is equal to the area enclosed by a square in a flat plane which is one mile on every side. square mile example to be eventually removed example to be eventually removed failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg Person:Alan Ruttenberg failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot core obsolete_core true placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. We expect to be able to mine these new reasons and add instances as required. obsolete_other true universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal universal defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg Alan Ruttenberg defined class defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg Alan Ruttenberg named class expression named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 out of scope "A time unit which is equal to 7 days." [Wikipedia:Wikipedia] week "An area unit which is equal to an area enclosed by a square with sides each 1 meter long." [NIST:NIST] square meter ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation ## Elucidation This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; ## How to interpret (informal) First the &quot;atemporal&quot; FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation axiom holds for all times true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts true GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' involved in BP If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).