Amanda Hicks John Levander Josh Hanna Matt Diller Mike Wagner Shawn T. Brown William R. Hogan Mathias Brochhausen Apollo Structured Vocabulary (Apollo-SV) An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. https://creativecommons.org/licenses/by/4.0/ 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). 2023-01-10 2023-06-02 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 label editor preferred term editor preferred term editor preferred term~editor preferred label example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage 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 has curation status has curation status definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition 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.obofoundry.org/obo/obi> editor note 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 term editor alternative label 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. OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label alternative term alternative term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source 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 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 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 . 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 instance unique identifier An annotation to be applied to individuals only. Value is a GUID/UUID for use in a referent tracking system. IUI term replaced by 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 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 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 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/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part 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 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 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 relationship 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 unfolds_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 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 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 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 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 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 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 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 x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context.. Mathias Brochhausen obsolete_designates true x is_borrowed_reference_for y, if x is a proper name that is used to refer to one individual among a specific group after the dubbing process took place. Mathias Brochhausen is_borrowed_reference_to x is_fixed_reference_for y, if x is an utterance or graphemes concretized as writing quality inhering in some independent continuant that is used to single out one individual and refer to the latter among a specific group after the. Mathias Brochhausen is_fixing_reference_to p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context. Mathias Brochhausen is designated by true 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 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. 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. http://purl.obolibrary.org/obo/omrse.owl is owned by http://purl.obolibrary.org/obo/omrse.owl is enrolled in school http://purl.obolibrary.org/obo/omrse.owl is admitted to hospital inheres in this fragility is a characteristic of this vase 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. 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 bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of 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 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 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/ location_of location of contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained_in contained in contains contains 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/ located_in http://www.obofoundry.org/ro/#OBO_REL:located_in 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. dos 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. dos 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. dos 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 dos 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. dos 2017-05-24T09:49:21Z has component process dos 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. GOC:dos 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. dos 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. GOC:dos 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. dos 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. GOC:dos 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. dos 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. GOC:dos 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 X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). 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. GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false 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) 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) 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 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 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 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 inverse of enables 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 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 p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly inhibits 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 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. GOC:cjm GOC:dos 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 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 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 2018-01-26T23:49:51Z 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 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 2018-03-13T23:55:05Z 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 RO:cjm 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. pg 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. pg 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 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 migration 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. Insecticid