Amanda Hicks John Levander Josh Hanna Matt Diller Mike Wagner Shawn T. Brown William R. Hogan Mathias Brochhausen Apollo Structured Vocabulary (Apollo-SV) 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). 2022-11-25 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 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 BFO OWL specification label 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 editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example of usage example of usage has curation status has curation status definition definition textual definition editor note editor note definition editor definition editor term editor term editor alternative term alternative term definition source definition source has obsolescence reason curator note curator note imported from expand expression to OBO foundry unique label elucidation has associated axiom(nl) has associated axiom(fol) ISA alternative term NIAID GSCID-BRC alternative term temporal interpretation 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 Creator Source Source dc:type has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym 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 obsolete_is_realized_by 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_as realized by realized_by http://purl.obolibrary.org/obo/obi.owl is realized by realizes 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 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 occurs in unfolds_in contains-process containsProcess [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 contains process is aggregate of aggregate of aggregate_of http://purl.obolibrary.org/obo/obi.owl is aggregate of exists at 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 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 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 has-t-ppart http://purl.obolibrary.org/obo/bfo.owl has proper temporal part history of has history has measurement unit label is about relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of 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 true true true 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 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 bearer of bearer_of http://purl.obolibrary.org/obo/omrse.owl is bearer of has_participant has_participant is_concretization_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) 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 immediately_preceded_by 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 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 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 'heart development' has active participant some Shh protein 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 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 move to BFO? Allen http://purl.obolibrary.org/obo/obi.owl A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporal relation temporally related to 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. started by http://purl.obolibrary.org/obo/obi.owl starts with inverse of ends with 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. finished with http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl ends with 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 inverse of upstream of Chris Mungall http://purl.obolibrary.org/obo/ro.owl causally downstream of p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall http://purl.obolibrary.org/obo/ro.owl causally upstream of 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. 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 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 has measurement 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 resulting in a software product involving the creation of source code. 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 simulation of 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 in which the parameter μ is the mean or expectation of the distribution and the parameter σ is its standard deviation 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. 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 2 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 2 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 2 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 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. 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. InsecticideTreatedNetControlMeasure insecticide-treated net control measure A plan specification that specifies 1) the quantity of which some material entity will be allocated to the eventual realization of some action specification, and 2) the temporal regions in which each action specification is to be realized. Matthew Diller William R. Hogan A plan specification that specifies 1) the quantity of which some material entity will be allocated to the eventual realization of some action specification, and 2) the temporal regions in which each action specification is to be realized. Schedule schedule A population census about the organisms specific to that population that were the host in some colonization acquisition. Matthew Diller William R. Hogan A population census about the organisms specific to that population that were the host in some colonization acquisition. PopulationColonizationCensus population colonization census The efficacy measured for some instance(s) of drug treatment for preventing or ameliorating some disease outcome. Matthew Diller William R. Hogan The efficacy measured for some instance(s) of drug treatment for preventing or ameliorating some disease outcome. drugTreatmentEfficacy While we understand that 'drug efficacy' can have multiple interpretations, this class is specifically referring to drug efficacy in the context of clinical outcomes. As such, our definition excludes any mention of efficacy as it relates to pharmacodynamics. drug treatment efficacy A data set that comprises exactly one latitude measurement datum and exactly one longitude measurement datum as its elements, and optiionally the geodetic datum used as the coordinate system for the measurements, and each of these measurements is about the same zero-dimensional geographical region. Matthew Diller William R. Hogan A data set that comprises exactly one latitude measurement datum and exactly one longitude measurement datum as its elements, and optiionally the geodetic datum used as the coordinate system for the measurements, and each of these measurements is about the same zero-dimensional geographical region. LatLongPair latitude and longitude coordinate pair A time measurement datum that refers to the temporal interval occupied by the life course of some organism and that takes 'years' as its measurement unit label. Matthew Diller William R. Hogan A time measurement datum that refers to the temporal interval occupied by the life course of some organism and that takes 'years' as its measurement unit label. ageInYears age in years datum A duration that measures a temporal region occupied by some contamination. Matthew Diller William R. Hogan A duration that measures a temporal region occupied by some contamination. contaminationDuration contamination period duration A healthcare facility identifier that refers to some architectural structure that is the bearer of some healthcare function. Matthew Diller William R. Hogan A healthcare facility identifier that refers to some architectural structure that is the bearer of some healthcare function. healthcareFacilityId healthcare facility identifier An identifier that refers to some disease transmission model model. Matthew Diller William R. Hogan An identifier that refers to some disease transmission model model. modelId disease transmission model identifier An identifier that denotes some architectural structure. Matthew Diller William R. Hogan An identifier that denotes some architectural structure. FacilityId facility identifier An identifier that denotes a biological taxonomic group. Matthew Diller William R. Hogan taxonId taxonomy identifier An identifier that denotes an organism included in some infection case count. Matthew Diller William R. Hogan An identifier that denotes an organism included in some infection case count. caseId disease case identifier An infection acquistion from infectious host that is causally downstream of some potentially infectious sexual contacting Matthew Diller Note that infections that are acquired in this manner do not fall within the class of sexually transmitted infections (STI's), ipso facto. This type of transmission can also occur with non-STI pathogens--such as meningitis and Zika. infection acquisition through sexual activity with infectious host A rate measurement datum that is the result of the measurement of the volume of water produced by some hydrological precipitation process at a particular geographical region divided by the number of temporal intervals of equal duration over which the precipitation occurred. Matthew Diller William R. Hogan rate of hydrological precipitation An average value that takes, as input, some set of rate of hydrological precipitation data that were recorded over a particular duration of time. Matthew Diller William R. Hogan mean rate of hydrological precipitation An average value that takes, as input, some set of air temperature measurement data that were recorded over a particular duration of time. Matthew Diller William R. Hogan mean air temperature A sexual activity with at least one infectious host as participant where the infectious host(s) are infected with a pathogen that has a disposition to infect the tissues of the non-infected host that came into physical contact with the infectious host during the activity. Matthew Diller William R. Hogan potentially infectious sexual contacting host population A population of organisms some of which were susceptible to infection with a particular pathogen at some point in their lives. William R. Hogan population of host organisms host population An action specification that is part of an infectious disease control strategy that has at least one rule pertaining to some control measure. Matthew Diller William R. Hogan An action specification that is part of an infectious disease control strategy that has at least one rule pertaining to some control measure. controlMeasureNamedPrioritizationScheme prioritization scheme for control measure A data transformation that takes as its input exactly one continuous variable as a value and assesses whether any statistically significant change to that variable will produce some change to the model's output. Matthew Diller William R. Hogan A data transformation that takes as its input exactly one continuous variable as a value and assesses whether any statistically significant change to that variable will produce some change to the model's output. Class was originally created to correspond with a complex type from Apollo XSD v3.1.0. one-way sensitivity analysis of a continuous variable An identifier that is an integer numeral that denotes some citation. Matthew Diller William R. Hogan An identifier that is an integer numeral that denotes some citation. referenceId citation identifier A geographic region that contains a sampling process. Matthew Diller William R. Hogan A geographic region that contains a sampling process. whereSampled location of sampling process An infection acquisition from infectious host by an embryo, fetus, or baby from its infectious mother while in utero, in egg at any point prior to hatching (even after laying), or during childbirth. Matthew Diller William R. Hogan congenital infection acquisition infection acquisition from mother-to-child transmission An infection acquisition from infectious host by an embryo, fetus, or baby from its infectious mother while in utero, in egg at any point prior to hatching (even after laying), or during childbirth. infection acquisition from vertical transmission software source code version control repository A data set that comprises at least one set of source code files for software as well as provenance information about who contributed the set of files, and optionally multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc. William R. Hogan Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based source code repository process of compiling software A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions. William R. Hogan It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.). Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code. compiling software machine instructions compiled from software source code A software that is the specified output of some compilation of software process William R. Hogan compiled software code An algorithm that models some scale-free network. Matthew Diller William R. Hogan scale-free network model A graph of vertices in which, for some fraction of vertices, P(k), the number of connections, k, varies as a power of some parameter, γ. In other words, P(k) ~ k^(-γ), where 2 < γ < 3. Matthew Diller William R. Hogan scale-free network A data set that represents 1) one or more collections of organisms at some time and some geographical region; and optionally 2) the school facilities, workplace facilities, and health care facilities in that region. Matthew Diller William R. Hogan SyntheticEcosystem The interactions between each organism as they move between these facilities may also be included in the data set. synthetic ecosystem data set A probability whose value is dependent upon the occurrence, known or presumed, of some process. Matthew Diller William R. Hogan A probability whose value is dependent upon the occurrence, known or presumed, of some process. conditionalProbability conditional probability A conditional probability whose value is dependent upon the duration of some colonization or infection. Matthew Diller William R. Hogan A conditional probability whose value is dependent upon the duration of some colonization or infection. probabilityOfInfectionOverTime probability of infection over time A data item that specifies the number of susceptible organisms necessary for an epidemic to occur within a population. Matthew Diller William R. Hogan epidemic threshold A geographical migration of an organism belonging to the species Homo sapiens. Matthew Diller William R. Hogan human travel Human travel that involves 1) movement from one geographical region to another through the air as a temporal proper part, and 2) the use of some processed material (e.g., airplane, hang glider) for propulsion that has some function of mechanical flight. Matthew Diller William R. Hogan human air travel A data item that is about one or more instances of human travel, and that specifies the geographical start location, geographical end location, and the geographical regions visited throughout the process. Matthew Diller William R. Hogan human mobility data item A copyright license that is about some software and contains one or more conditional specifications that specify the use and redistribution of the software. Matthew Diller William R. Hogan A copyright license that is about some software and contains one or more conditional specifications that specify the use and redistribution of the software. software license An identifier that refers to a specific software license. Matthew Diller William R. Hogan An identifier that refers to a specific software license. SoftwareLicenseIdentification complete software license identifier An identifier that, as part of a complete software license identifier, refers to one specific version of the software license. Matthew Diller William R. Hogan An identifier that, as part of a complete software license identifier, refers to one specific version of the software license. licenseVersion software license version identifier An identifier that refers to all versions of a specific software license. Matthew Diller William R. Hogan An identifier that refers to all versions of a specific software license. licenseName software license identifier A unique resource locator that constitutes a reference to some software license. Matthew Diller William R. Hogan A unique resource locator that constitutes a reference to some software license. licenseLocation software license URL model of population dynamics software application An simulation software application that when realized simulates changes in the size and life stage distribution of a population or populations of organisms of a particular biological taxon. Matthew Diller William R. Hogan An algorithm that simulates changes in the size and life stage distribution of a population or populations of organisms of a particular biological taxon. population dynamics model disease surveillance objective specification An objective specification whose endpoint is human awareness of the level of a particular disease in a particular population of a given biological taxon during some time interval. Matthew Diller William R. Hogan An objective specification whose endpoint is human awareness of the level of a particular disease in a particular population of a given biological taxon during some time interval. disease surveillance objective specification population mortality data set A data set that is about either some mortality rate or the death events themselves of some individuals of a given population of a particular biological taxon. Matthew Diller William R. Hogan A data set that is about either some mortality rate or the death events themselves of some individuals of a given population of a particular biological taxon. mortality data pathogen evolution model software application A simulation software application that simulates the evolution over time of a particular pathogen of a particular biological taxon. Matthew Diller William R. Hogan Simulation software that simulates the evolution over time of a particular pathogen of a particular biological taxon. pathogen evolution model A planned process that is the realization of a disease surveillance objective specification. Matthew Diller William R. Hogan A planned process that is the realization of a disease surveillance objective specification. disease surveillance Individual human behavior that involves either 1) remaining in some susceptible population or some exposed population or 2) human movement away from or around an infectious population, in order to avoid being participant in some infection acquisition. Matthew Diller William R. Hogan Individual human behavior that involves either 1) remaining in some susceptible population or some exposed population or 2) human movement away from or around an infectious population, in order to avoid being participant in some infection acquisition. self-initiated travel avoidance behavior A data item that is about one or more instances of social interaction between two or more individuals, and that specifies the temporal duration of interaction, spatial distance of individuals, geographical location of individuals, and the number of individuals participant in some social behavior(s). Matthew Diller William R. Hogan A data item that is about one or more instances of social interaction between two or more individuals, and that specifies the temporal duration of interaction, spatial distance of individuals, geographical location of individuals, and the number of individuals participant in some social behavior(s). social interaction data item A compartmental disease transmission model that represents some infection in ecosystem in which there is only a susceptible population and an infectious population, such that individuals who aren't infectious are susceptible. Matthew Diller William R. Hogan A compartmental disease transmission model that represents some infection in ecosystem in which there is only a susceptible population and an infectious population, such that individuals who aren't infectious are susceptible. Susceptible-Infected-Susceptible model A compartmental disease transmission model that represents some infection in ecosystem in which there are compartments for susceptible individuals, infectious individuals, and recovered individuals, such that recovered individuals are immune to future infection. Matthew Diller William R. Hogan A compartmental disease transmission model that represents some infection in ecosystem in which there are compartments for susceptible individuals, infectious individuals, and recovered individuals, such that recovered individuals are immune to future infection. Susceptible-Infected-Resistant model An infectious disease control strategy that identifies and treats contacted organisms in a host population. Matthew Diller William R. Hogan An infectious disease control strategy that identifies and treats contacted organisms in a host population. contact tracing A compartmental disease transmission model that represents some infection in ecosystem in which there are compartments for susceptible individuals, exposed individuals, infectious individuals, and immune inviduals, such that exposed individuals are infected but cannot transmit the pathogen. Matthew Diller William R. Hogan A compartmental disease transmission model that represents some infection in ecosystem in which there are compartments for susceptible individuals, exposed individuals, infectious individuals, and immune inviduals, such that exposed individuals are infected but cannot transmit the pathogen. Susceptible-Exposed-Infectious-Recovered model A disease transmission model that is about two or more collections of organisms of a particular biological taxon in separate geographical locations and some geographical migration of organisms between them. Matthew Diller William R. Hogan A disease transmission model that is about two or more collections of organisms of a particular biological taxon in separate geographical locations and some geographical migration of organisms between them. metapopulation disease transmission model A Susceptible-Infected-Resistant model that represents exactly two infections in ecosystem by exactly two pathogens. Matthew Diller William R. Hogan A Susceptible-Infected-Resistant model that represents exactly two infections in ecosystem by exactly two pathogens. two-strain Susceptible-Infectious-Resistant model A data set that is about some disease surveillance. Matthew Diller William R. Hogan A data set that is about some disease surveillance. disease surveillance data disease transmission tree estimator software application A software application that implements an algorithm that has specified output some transmission tree. Matthew Diller William R. Hogan An algorithm that has specified output some transmission tree. disease transmission tree estimator A function inhering in some device that is realized by some movement process in the atmosphere in which the device is participant in. Matthew Diller William R. Hogan A function inhering in some device that is realized by some movement process in the atmosphere in which the device is participant in. mechanical flight function software application that forecasts disease transmission A simulation software application that has as output one or more predicted count data items that are about a host population and that predict how many infections will occur at or will have occurred at some temporal region relative to when the data items are created. Matthew Diller William R. Hogan disease forecasting software infectious disease forecaster infectious disease forecasting software application An investigation that realizes the concretization of some disease state design and that has as an occurrent part some population survey that has specified input some case definition. Matthew Diller William R. Hogan An investigation following a disease state study design that includes a population survey as part, where a case definition used in the population survey to ascertain disease state. CaseSeries case series A data set that is the output of a case series investigation. Matthew Diller William R. Hogan A data set that is the output of a case series investigation. case series data set A data set about an instance of an epidemic. Matthew Diller William R. Hogan A data set about an instance of an epidemic. epidemic data set disease transmission model software application Matthew Diller William R. Hogan disease transmission model software data format converter software application Matthew Diller William R. Hogan data format converter phylogenetic tree constructor software application A software application that implements an algorithm that has specified output a phylogenetic tree William R. Hogan phylogenetic tree constructor data visualizer software application A software application that implements an algorithm that has some data visualizer software objective specification as part. Matthew Diller William R. Hogan data visualizer computational modeling toolkit software application Matthew Diller William R. Hogan computational modeling toolkit data parsing process A data transformation that has a dataset, encoded in a particular data format specification, as input and extracts certain elements or parts of the dataset, typically into the volatile memory of a computer. William R. Hogan data reading process reading data data parsing synthetic ecosystem constructor software A software that when compiled and run, has specified output of an agent-level ecosystem data set. William R. Hogan software for creating a synthetic ecosystem dataset example: Synthia, SPEW synthetic ecosystem constructor A data item that is the output of some infection case count and that represents the number of infectious disease cases that ended in death. Matthew Diller William R. Hogan A data item that is the output of some infection case count and that represents the number of infectious disease cases that ended in death. totalFatalCaseCount total fatal disease cases A count of the total number of diseased indivduals in a population during a particular time interval. Matthew Diller William R. Hogan The total number of diseased individuals in a population at a point in time. totalCaseCount total disease cases A data item that denotes some context in which an individual realizes some employee role if he or she is a member of the labor force, or the context in which he or she is not a member of the labor force according to certain prespecified conditions. Matthew Diller William R. Hogan A data item that denotes some context in which an individual realizes some employee role if he or she is a member of the labor force, or the context in which he or she is not a member of the labor force according to certain prespecified conditions. employmentStatus If an individual is a member of the labor force, the criteria that this status is selected from includes whether they are in the armed forces, employed and working, employed but absent from work for a week, and unemployed. The criteria for those not in the labor force includes whether the individual is a houseworker, suffering from a physical impairment that prevents them from working, in school, or other miscellaneous reasons. employment status data item An abiotic ecosystem element that is participant in some biological contamination process. Matthew Diller William R. Hogan An abiotic ecosystem element that is participant in some biological contamination process. contaminatedAbioticThing contaminated abiotic thing An adult vector control strategy that has 1) an action specification that is realized by the use of mosquito traps that leverage natural or synthetic human odors as bait, and 2) an objective specification that is realized by preventing potentially infectious contacting between some mosquito vector and some human host. Matthew Diller William R. Hogan An adult vector control strategy that has 1) an action specification that is realized by the use of mosquito traps that leverage natural or synthetic human odors as bait, and 2) an objective specification that is realized by preventing potentially infectious contacting between some mosquito vector and some human host. odor-baited trap control strategy An infectious disease control strategy that attempts to prevent infection of susceptible human host organisms in a particular geographical region by increasing the population of domesticated animals in that region, such that less mosquitoes feed on humans. Matthew Diller William R. Hogan An infectious disease control strategy that attempts to prevent infection of susceptible human host organisms in a particular geographical region by increasing the population of domesticated animals in that region, such that less mosquitoes feed on humans. zoo-prophylaxis control strategy A clinical phenotype that is causally preceded by some infection or some adverse drug reaction; and that is accompanied by a fever greater than or equal to 37.8 degrees Celsius, and a cough or sore throat. Matthew Diller William R. Hogan influenza-like illness acute respiratory illness A scalar value specification whose measurement unit label is 'week' and that is part of the first predicted data item that is greater than the epidemic threshold set for that data item. Amanda Hicks Matthew Diller William R. Hogan epidemic start week A scalar value specification whose measurement unit label is 'week', and that is part of the epidemic peak intensity. Amanda Hicks Matthew Diller William R. Hogan epidemic peak week A predicted data item that is about some aggregate of cases in an epidemic and whose value specification contains the maximum value in a data set that is about the epidemic. Amanda Hicks Matthew Diller William R. Hogan epidemic peak intensity A process that (1) has as occurrent parts at least two disease courses that realize the same type of disease, and (2) has as participants two or more hosts that are members of a particular host population. Amanda Hicks Matthew Diller William R. Hogan aggregate of disease courses A planned process that realizes some infectious disease forecasting software. Matthew Diller William R. Hogan infectious disease forecast An infectious disesae forecast that realizes some infectious disease nowcasting software. Matthew Diller William R. Hogan infectious disease nowcast An objective specification that is realized by the estimation of one or more predicted data items that are about 1) some infection in ecosystem and 2) potential changes to its number of participants (e.g., individuals within a host population, individuals within a vector population) relative to a particular temporal region; and is part of some infectious disease forecasting software. Matthew Diller William R. Hogan infectious disease forecast objective specification An infectious disease forecasting objective specification that is realized by the estimation of one or more predicted data items that are about some infection in ecosystem as they are occurring in real time, and is part of some infectious disease nowcasting software. Matthew Diller William R. Hogan infectious disease nowcast objective specification infectious disease nowcasting software application An infectious disease forecasting software application that predicts how many infections are occurring within the same temporal interval that the data items are being estimated. Matthew Diller William R. Hogan infectious disease nowcaster An infectious disease forecast that has specified input some data set, the data items of which are about an infection in ecosystem that is current concomitant with the forecasting software’s executable code being realized. Matthew Diller William R. Hogan prospective infectious disease forecast An infectious disease nowcast that has specified input some data set, the data items of which are about an infection in ecosystem that is current concomitant with the forecasting software’s executable code being realized. Matthew Diller William R. Hogan prospective infectious disease nowcast An action specification that specifies the duration of time that is to elapse between each calculation of each predicted data item that is the output of some infectious disease forecast. Matthew Diller William R. Hogan infectious disease forecast time specification An inpatient encounter in which the health care provider role is realized by some person employed by the intensive care department of some health care facility, and the patient role is realized by someone admitted to that intensive care department. intensive care unit encounter An objective specification that is realized when a diagram is drawn from one or more data sets. Matthew Diller William R. Hogan data visualization objective specification treatment in the intensive care unit control strategy an individual treatment control strategy that is realized by one or more intensive care unit encounters for infected individuals in the population William R. Hogan an individual treatment control strategy that is realized by treating one or more infected individuals in an intensive care unit treatment in the ICU control strategy website that has data as a part William R. Hogan This class was created for use case for MIDAS Digital Repository to index websites that have useful data in them, albeit rarely as machine-interpretable, downloadable datasets. Much of the data are locked in PDF or other text-based formats. website with data climate data set A data set that is an aggregate of data items that are about an environmental system process (e.g., hydrological precipitation) or a participant in an environmental system process. Matt Diller William R. Hogan climate data set metagenomics analysis software application Matthew Diller William R. Hogan A software application that has as part an objective specification that is achieved by only a metagenomics analysis. metagenomics analysis software abiotic ecosystem data set A data set that is about some abiotic ecosystem or abiotic ecosystem element. William R. Hogan abiotic ecosystem dataset data set about an abiotic ecosystem or abiotic ecosystem element A data set that is about an abiotic ecosystem or some abiotic ecosystem element. abiotic ecosystem data set atmospheric data set A data set that is about either the Earth's atmosphere or some part of the Earth's atmosphere. William R. Hogan A data set that is about either the Earth's atmosphere or some part of the Earth's atmosphere. atmospheric data set data set about Earth's atmosphere or some part of it census of treatment facility A census that counts the number of treatment facilities of some kind in a particular geographical region. William R. Hogan census of treatment facilities treatment facilities census treatment facility census A census that counts the number of treatment facilities of some kind in a particular geographical region. NOTE: this class counts the facilities themselves, not patients (people) in those facilities. For example, how many hospitals in a state. Not how many patients are in a hospital or hospitals in a state. treatment facility census 2 symbiosis An interspecies interaction between two or more organisms in intimate association. Matthew Diller William R. Hogan Martin BD, Schwab E. Current usage of symbiosis and associated terminology. International Journal of Biology. 2013 Jan 1;5(1):32. Available from: https://web.archive.org/web/20190723160720/https://www.researchgate.net/publication/233865641_Current_Usage_of_Symbiosis_and_Associated_Terminology By "intimate interaction," we mean any interaction between two or more organisms that involves (1) physical contact or (2) multi-organism behavior in which all interacting organisms are participant. symbiosis data format validator software application A software application that takes a data set as input and outputs a determination of whether the dataset is in compliance with one or more given data format specifications. William R. Hogan data format validator disease identifier an identifier that denotes a disease. William R. Hogan Mathias Brochhausen 2021-03-16T16:01:41Z disease identifier dataset about infectious disease acquisitions The dataset at this link is rdf:type this class: https://figshare.com/articles/dataset/COVID19_settings_of_transmission_-_collected_reports_database/12173343 a dataset that is about infectious disease acquisitions at particular times and particular places. William R. Hogan 2021-03-16T16:16:26Z The dataset may include sites (e.g. types of facilities, rooms), events (e.g., church service whether in or outdoors), dates, times, geographical regions, etc. in which the sites/events are located, and so on. infection acquisition dataset dataset about hospital stays The datasets at this link are rdf:type this class: https://www.opendataphilly.org/dataset/covid-hospitalizations a dataset that is about two or more hospital stays involving two or more patients. William R. Hogan hospital discharge dataset hospitalization dataset 2021-03-16T16:20:48Z The dataset may be limited to stays in one hospital, but hospital discharge datasets as compiled by state departments of health typically contain stays from multiple hospitals (typically every hospital) in the geographical region over which they have jurisdiction hospital stay dataset human daily movement behavior an individual human behavior that is the movements from one location to another throughout the day (e.g., work, home, stores, church, relatives' homes) in the areas adjacent to where the human lives at the time. William R. Hogan 2021-03-16T16:29:53Z human daily movement human daily movement behavior data set https://www.google.com/covid19/mobility/ a data set that is about the human daily movement behavior of the individual huamns in a given population. William R. Hogan 2021-03-16T16:32:39Z human daily movement data set potentially infectious contact process data set in a population a data set that is about one or more potentially infectious contact processes in a population of host organisms. William R. Hogan contact data set 2021-03-16T16:39:24Z potentially infectious contact data set infectious disease control strategy census a census of infectious disease control strategies put into place to reduce infection acquisitions that are part of an infection in an ecosystem. William R. Hogan 2021-03-16T16:43:04Z control strategy census school closure infectious disease control strategy census an infectious disease control strategy census that is about school closure infectious disease control strategies implemented in a particular geographical region. William R. Hogan 2021-03-16T16:44:03Z This class represents datasets about strategies for school closure. Datasets about individual actual school closures go elsewhere. school closure control strategy census vaccination infectious disease control strategy census William R. Hogan 2021-03-16T16:47:09Z This class is an inventory of vaccination control strategies, not vaccinations themselves. So it should be a list of things like "Publix vaccination plan", "Alachua county vaccination plan", "Sam's Club vaccination plan", etc. And not a list of individual vaccinations given to actual patients (see population vaccination census) vaccination control strategy census population vaccination census vaccine / immunization registry data, vaccination / immunization records extracted from an EHR a population treatment census that is about one or more vaccinations of organisms in a population. William R. Hogan vaccination census 2021-03-16T16:48:42Z vaccination administration census dataset about excess mortality in a population A population mortality dataset that compares deaths in the population during one time interval to deaths in the population during a previous time interval and reports an estimate of how many more or less deaths occurred in the later time interval. William R. Hogan Often used during epidemics or pandemics to estimate the death toll. excess mortality dataset census of supplies of vaccine products A control strategy inventory census that counts available vaccine doses of one or more similar vaccines. William R. Hogan vaccine availability https://orcid.org/0000-0002-9881-1017 2022-02-01T00:03:00Z Motivated my MIDAS coordination center indexing of COVID-19 data, software, etc. By "similar vaccines" we typically mean same pathogen, but could be similar in other ways (requiring refrigeration of a certain kind). census of vaccination supplies census of facilities that conduct clinical laboratory tests A census of facilities that conduct clinical laboratory testing. William R. Hogan testing availability https://orcid.org/0000-0002-9881-1017 2022-02-01T00:10:00Z The census might also include information about each facility such as operating hours, address, accessibility, and so on. laboratory testing facility census model for disease transmission parameter estimation An algoirthm that is used to estimate the "true" values of certain parameters of disease transmission and/or forecasting. William R. Hogan 2022-09-18T17:51:00 Examples of parameters estimated include R0, transmissibility, infectious period. parameter estimation model An algorithm that operates on a representation of some portion of reality and that representation has a structure with nodes that stand for certain entities and edges that state some direct or indirect relationship between pairs of entities. William R. Hogan 2022-09-18T18:00:00 The algorithm might involve also generating or creating the network structure in addition to operating on it. network model laboratory testing capacity action specification An action specification giving the number of laboratory tests of a certain type that it is possible to perform in a given population during a specific time interval. William R. Hogan 2022-09-18T18:21 laboratory testing capacity data set about Earth's atmospheric weather A data set about the Earth's atmospheric weather William R. Hogan 2022-09-18T18:34:00 weather data set monkeypox disease inhering in a human being A monkeypox disease inhering in a human being. William R. Hogan 2022-09-18T18:51:00 requested by MIDAS CC human monkeypox epidemic simulator action specification William R. Hogan epidemic simulator action specification infectious disease control strategy action specification William R. Hogan infectious disease control strategy action specification individual treatment control strategy action specification William R. Hogan individual treatment control strategy action specification creating a data set A planned process that has a data set as its specified output. William R. Hogan data set creation dataset creation dataset creating creating a copyright license A planned process that has a copyright license as its specified output. William R. Hogan copyright license creation Note: for less than 24 hours, this class was a bit more specific to software licenses, but it did not have the equivalent class axiom during that time. creating a copyright license copyright license for a creative work A document that is about the legal rights, claims, and obligations of a legal person (person or organization) under copyright law, and how that legal person intends for those rights, claims, and obligations to be handled/managed by users of the creative work to which this document is attached. William R. Hogan Can be for any creative work including fiction. But the license itself is an ICE, and refers to real claims and obligations. copyright license data service software application A software application that implements a data service. William R. Hogan data service software TODO facultative role A role borne by an organism in virtue of the fact that it is in intimate association with one or more organisms of different species, and is realized by bodily benefit to that organism as an occurrent part of a symbiosis with the other organisms. This bodily benefit takes the place of the organism or some relatively isolated part of the organism realizing some normal homeostasis disposition itself. facultative role Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries. Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital Synonyms: substance aggregate object_aggregate Interval A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. history The usage or intended usage of a drug product to act against a viral infection of a host. antiviral drug A viral infectious disease that has_material_basis in Zika virus, which is transmitted_by Aedes aegypti mosquitoes and targets neural progenitor cells and neuronal cells in all stages of maturity and has_symptom fever, has_symptom rash, has_symptom headaches and has_symptom joint pain. http://purl.obolibrary.org/obo/doid.owl ICD10:U06 ICD10CM:A92.8 MESH:D000071243 Zika virus disease Zika fever A viral infectious disease that results_in infection, has_material_basis_in Dengue virus [NCBITaxon:12637] with four serotypes (Dengue virus 1, 2, 3 and 4), which are transmitted_by Aedes mosquito bite. The infection has_symptom fever, has_symptom severe headache, has_symptom severe pain behind the eyes, has_symptom joint pain, has_symptom muscle and bone pain, has_symptom rash, and has_symptom mild bleeding. http://purl.obolibrary.org/obo/doid.owl DOID:0050142 ICD10CM:A90 ICD9CM:061 MESH:D003715 NCI:C34528 SNOMEDCT_US_2016_03_01:154345006 SNOMEDCT_US_2016_03_01:266194002 SNOMEDCT_US_2016_03_01:38362002 UMLS_CUI:C0011311 Dengue Fever breakbone fever classic dengue disease_ontology classical dengue DOID:12205 dengue disease A dengue disease that occurs when a person experiences a second infection with a heterologous Dengue virus serotype, which is transmitted_by Aedes mosquito bite. The infection has_symptom hemorrhagic lesions of the skin, has_symptom thrombocytopenia, has_symptom reduction in the fluid part of the blood, and has_symptom high fever. http://purl.obolibrary.org/obo/doid.owl ICD10CM:A91 MESH:D019595 NCI:C34683 SNOMEDCT_US_2016_03_01:186598001 SNOMEDCT_US_2016_03_01:186599009 SNOMEDCT_US_2016_03_01:20927009 UMLS_CUI:C0019100 DHF disease_ontology Dengue haemorrhagic fever DOID:12206 dengue hemorrhagic fever A viral infectious disease that results in infection of primates, rodents and humans, located in skin, has_material_basis_in Monkeypox virus, which is transmitted by contact with the animal's blood, body fluids, rash, or with the body fluids of a sick person, transmitted by fomites, and transmitted by respiratory droplets. The infection has symptom fever, has symptom muscle ache, has symptom headache, and has symptom lymphadenopathy. http://purl.obolibrary.org/obo/doid/releases/2022-08-29/doid.owl GARD:10722 ICD10CM:B04 ICD9CM:059.01 MESH:D045908 NCI:C128421 SNOMEDCT_US_2021_09_01:240466002 UMLS_CUI:C0276180 url:http://www.cdc.gov/ncidod/monkeypox/factsheet2.htm disease_ontology DOID:3292 monkeypox A viral infectious disease that results_in infection, located_in respiratory tract, has_material_basis_in Influenzavirus A, has_material_basis_in Influenzavirus B, or has_material_basis_in Influenzavirus C, which are transmitted_by droplet spread of oronasal secretions during coughing, sneezing, or talking from an infected person. It is a highly contagious disease that affects birds and mammals and has_symptom chills, has_symptom fever, has_symptom sore throat, has_symptom runny nose, has_symptom muscle pains, has_symptom severe headache, has_symptom cough, and has_symptom weakness. http://purl.obolibrary.org/obo/doid.owl DOID:8468 ICD10CM:J11.1 ICD9CM:487 MESH:D007251 NCI:C53482 SNOMEDCT_US_2016_03_01:155559006 SNOMEDCT_US_2016_03_01:155562009 SNOMEDCT_US_2016_03_01:195931008 SNOMEDCT_US_2016_03_01:266353003 SNOMEDCT_US_2016_03_01:266393000 SNOMEDCT_US_2016_03_01:6142004 UMLS_CUI:C0021400 Influenza with non-respiratory manifestation (disorder) Influenza with other manifestations Influenza with other manifestations (disorder) Influenza with other manifestations NOS (disorder) flu influenza with non-respiratory manifestation disease_ontology DOID:8469 influenza a material entity (1) containing at least one scattered molecular aggregate as part (the active ingredient) and (2) that is the bearer of a clinical drug role William Hogan http://purl.obolibrary.org/obo/dron.owl William Hogan drug product A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. http://purl.obolibrary.org/obo/envo.owl portion of environmental material ENVO ENVO:00010483 Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. environmental material An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system. http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl ORCID:0000-0002-4366-3088 2013-04-07T14:35:18Z DOI:10.1186/2041-1480-4-43 envoPolar A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional. environmental condition Water vapour is a vapour which is the gas phase of water. http://purl.obolibrary.org/obo/envo.owl ORCID:0000-0002-4366-3088 2013-10-10T07:58:18Z aqueous vapor aqueous vapour water vapor ENVO ENVO:01000266 Perhaps a better relation between water vapour and water can be found in or added to RO? water vapour Atmospheric water vapour is water vapour that is part of an atmosphere. http://purl.obolibrary.org/obo/envo.owl ORCID:0000-0002-4366-3088 2013-10-10T08:22:07Z atmospheric water vapor ENVO ENVO:01000268 atmospheric water vapour Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity. http://purl.obolibrary.org/obo/envo.owl precipitation "process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet) hydrological precipitation process A temperature that inheres in some portion of air. Draft class. In discussion in Issue #278. http://purl.obolibrary.org/obo/envo.owl air temperature A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely. This class is to be populated by inference. http://purl.obolibrary.org/obo/envo.owl gas gaseous environmental material Environmental variability which inheres in an astronomical body part or in outer space. http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl https://en.wikipedia.org/wiki/Space_weather https://en.wikipedia.org/wiki/Weather This class refers to all weather, including atmospheric and space weather. Please use a subclass for more specificity. weather Weather which inheres in an atmosphere. http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl https://en.wikipedia.org/wiki/Weather This class refers to the common usage of "weather", referencing the state of a (part of) an astronomical body's atmosphere. atmospheric weather A condition which inheres in an environmental system by virtue of that system undergoing variation in its composition, the distribution of the qualities its components bear, and/or in the processes which occur within it and which it participates in. http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl This class is very general, but the nature of environmental variability is indeed quite variable. This class may be refined once we have more subclasses to consider. environmental variability http://purl.obolibrary.org/obo/envo.owl Should environmental feature become something more towards a disposition, the assert would be updated to something like "has participant (environmental system or (material entity and has disposition some environmental feature))". There are several issues surrounding the reconcilliation of environmental feature and environmental system, both theoretical and practical. environmental system process The temperature of a environmental material. http://purl.obolibrary.org/obo/envo.owl environmental material temperature temperature of environmental material The temperature of a air. http://purl.obolibrary.org/obo/envo.owl air temperature temperature of air A molecular assay that is used to analyze metagenomic data; genetic material recovered directly from environmental samples for genomic research. PERSON: Nicole Vasilevsky community genomic analysis ecogenomic analysis environmental genomic analysis http://en.wikipedia.org/wiki/Metagenomics http://purl.obolibrary.org/obo/ero.owl metagenomics analysis A set of related web pages containing content such as text, images, video, audio, etc., prepared and maintained as a collection of information on a particular subject. http://purl.obolibrary.org/obo/fbcv.owl pub_type FBcv:0000667 website A publication issued on a regular, ongoing basis containing separate research articles and other writings such as reviews, comments and conference reports. http://purl.obolibrary.org/obo/fbcv.owl djs93 2012-07-10T04:08:06Z MeSH:D020492 pub_type Periodicals FBcv:0000787 journal definition is circular. A site designated by some relative spatial orientation. Matthew Diller William R. Hogan An arbitrary part of the Earth defined by human-made boundaries and/or natural features such as rivers. Location The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism. http://purl.org/obo/owl/gene_ontology The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism. Reproduction GO:0019952 GO:0050876 biological_process reproduction Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). http://purl.obolibrary.org/obo/go.owl biological_process response to abiotic stress response to biotic stress GO:0006950 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stress Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. http://purl.obolibrary.org/obo/go.owl GO:0002217 GO:0042829 defence response physiological defense response biological_process antimicrobial peptide activity defense/immunity protein activity GO:0006952 defense response The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. http://purl.obolibrary.org/obo/go.owl Inflammation Wikipedia:Inflammation biological_process GO:0006954 This term was improved by GO_REF:0000022. It was moved. inflammatory response The emergence of an adult insect from a pupa case. http://purl.org/obo/owl/gene_ontology biological_process eclose eclosion The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth. http://purl.obolibrary.org/obo/go.owl Wikipedia:Gestation gestation biological_process carrying of young GO:0007565 female pregnancy The reproductive process in which the parent is separated from its offspring either by giving birth to live young or by laying eggs. http://purl.obolibrary.org/obo/go.owl giving birth egg laying biological_process GO:0007567 parturition http://purl.org/obo/owl/gene_ontology GO:0016280 biological_process aging The internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. http://purl.obolibrary.org/obo/go.owl Behavior Wikipedia:Behavior behavioral response to stimulus behaviour behavioural response to stimulus biological_process GO:0007610 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. behavior The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes. http://purl.obolibrary.org/obo/go.owl Wikipedia:Mating_behaviour mating behaviour biological_process GO:0007617 mating behavior biological_process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. http://purl.obolibrary.org/obo/ido.owl biological process An aging process that has as participant a whole multicellular organism. Multicellular organism aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Multicellular organisms aging includes processes like cellular senescence and organ senescence, but is more inclusive. May precede death (GO:0016265) of an organism and may succeed developmental maturation (GO:0021700). http://purl.obolibrary.org/obo/go.owl biological_process GO:0010259 multicellular organismal aging Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. http://purl.obolibrary.org/obo/go.owl biological_process GO:0010941 regulation of cell death http://purl.org/obo/owl/gene_ontology biological_process oviposition The process in which a virus effects a change in the structure or processes of its host organism. http://purl.obolibrary.org/obo/go.owl GO:0044792 virus-host interaction Reactome:REACT_6323 VZ:886 host-virus interaction modulation by virus of host anatomical structure or process modulation by virus of host anatomy or process viral interaction with host viral-host process virus-host process biological_process GO:0019048 modulation by virus of host morphology or physiology The set of viral processes that induce an apoptotic process in infected host cells, facilitating release and spread of progeny virions. http://purl.obolibrary.org/obo/go.owl activation by virus of host apoptosis activation by virus of host apoptotic programmed cell death activation of apoptosis in host by virus induction by virus of host apoptotic programmed cell death induction of apoptosis in host by virus induction by virus of host apoptosis biological_process GO:0019051 induction by virus of host apoptotic process The process in which a virus effects a change in the processes and activities of its host organism. http://purl.obolibrary.org/obo/go.owl Reactome:REACT_6222 modification by virus of host cellular process regulation by virus of host cellular process regulation of cellular process in host by virus regulation of host cellular process by virus viral host cell process manipulation biological_process modulation of cellular process in host by virus GO:0019054 modulation by virus of host process http://purl.org/obo/owl/gene_ontology biological_process reproductive behavior A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. http://purl.obolibrary.org/obo/go.owl biological_process GO:0022414 reproductive process http://purl.org/obo/owl/gene_ontology biological_process developmental process The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. http://purl.obolibrary.org/obo/go.owl biological_process GO:0032504 multicellular organism reproduction http://purl.org/obo/owl/gene_ontology biological_process multicellular organismal reproductive behavior Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. http://purl.obolibrary.org/obo/go.owl Wikipedia:Social_behavior social behaviour biological_process cooperative behavior GO:0035176 Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. social behavior The process in which an organism effects a change in the structure or processes of a second organism. http://purl.obolibrary.org/obo/go.owl rfoulger 2011-04-21T01:31:51Z regulation of morphology of other organism regulation of physiological process of other organism regulation of physiology of other organism biological_process regulation of morphology or physiology of other organism GO:0035821 modification of morphology or physiology of other organism Any process in which a virus increases the frequency, rate or extent of host cysteine-type endopeptidase activity (also called caspase activity) which contributes to the apoptotic process. http://purl.obolibrary.org/obo/go.owl rfoulger 2012-10-09T15:44:29Z activation of host caspases by virus induction by virus of host caspase activity biological_process GO:0039651 induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. http://purl.obolibrary.org/obo/go.owl GO:0043070 regulation of non-apoptotic programmed cell death biological_process GO:0043067 regulation of programmed cell death The process in which a symbiont organism effects a change in the structure or processes of its host organism. http://purl.obolibrary.org/obo/go.owl biological_process GO:0044003 modification by symbiont of host morphology or physiology Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. entry into host Any process in which an organism has an effect on an organism of a different species. interspecies interaction between organisms A process in which an organism modulates the frequency, rate or extent of programmed cell death in a second organism. http://purl.obolibrary.org/obo/go.owl janelomax 2012-03-20T04:48:41Z biological_process GO:0044531 modulation of programmed cell death in other organism A biological process that directly contributes to the process of producing new individuals, involving another organism. http://purl.obolibrary.org/obo/go.owl janelomax 2012-09-19T15:56:30Z biological_process GO:0044703 multi-organism reproductive process The specific behavior of an organism that is associated with reproduction involving another organism of the same or different species. http://purl.obolibrary.org/obo/go.owl janelomax 2012-09-19T16:02:12Z biological_process GO:0044705 multi-organism reproductive behavior The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. http://purl.obolibrary.org/obo/go.owl organismal reproductive process reproductive process in a multicellular organism biological_process GO:0048609 multicellular organismal reproductive process Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. http://purl.obolibrary.org/obo/go.owl GO:0050791 regulation of physiological process biological_process GO:0050789 regulation of biological process Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. http://purl.obolibrary.org/obo/go.owl GO:0051244 regulation of cellular physiological process biological_process GO:0050794 regulation of cellular process Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. http://purl.obolibrary.org/obo/go.owl GO:0051869 physiological response to stimulus biological_process GO:0050896 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stimulus establishment of localization The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location. http://purl.obolibrary.org/obo/ido.owl establishment of localization establishment of localization An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism. http://purl.obolibrary.org/obo/go.owl biological_process GO:0051701 interaction with host A biological process which involves another organism of the same or different species. multi-organism process Any process in which an organism has a behavioral effect on another organism of the same or different species. http://purl.obolibrary.org/obo/go/releases/2019-07-01/go.owl GO:0023032 GO:0044709 GOC:ai GOC:mah behavioral interaction between organisms behavioral interaction with other organism behavioural interaction between organisms behavioural interaction with other organism behavioral signaling behavioral signalling biological_process GO:0051705 multi-organism behavior The process in which an organism effects a change in the structure or processes of a second organism, where the two organisms are in a symbiotic interaction. http://purl.obolibrary.org/obo/go.owl regulation of morphology of other organism during symbiotic interaction regulation of physiological process in other organism during symbiotic interaction regulation of physiology of other organism during symbiotic interaction biological_process modification of morphology or physiology of other organism during symbiotic interaction modulation of morphology or physiology of other organism during symbiotic interaction regulation of morphology or physiology of other organism during symbiotic interaction GO:0051817 modification of morphology or physiology of other organism involved in symbiotic interaction Any process in which an organism modulates the frequency, rate or extent of programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. http://purl.obolibrary.org/obo/go.owl GO:0052152 modulation of host PCD modulation by symbiont of host non-apoptotic programmed cell death biological_process GO:0052040 modulation by symbiont of host programmed cell death Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. http://purl.obolibrary.org/obo/go.owl GO:0012504 GO:0052044 GO:0052045 GO:0052153 GO:0052397 GO:0052400 activation by organism of host programmed cell death activation by organism of programmed cell death in other organism during symbiotic interaction enhancement of host programmed cell death enhancement of host programmed cell death by organism induction by organism of programmed cell death in other organism involved in symbiotic interaction induction by symbiont of host programmed cell death upregulation by symbiont of host programmed cell death activation by organism of non-apoptotic programmed cell death in other organism activation by symbiont of host programmed cell death induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction positive regulation by symbiont of host non-apoptotic programmed cell death stimulation by symbiont of host programmed cell death biological_process induction by organism of programmed cell death in other organism during symbiotic interaction induction of non-apoptotic programmed cell death by other organism GO:0052042 positive regulation by symbiont of host programmed cell death Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death in the host, where programmed cell death proceeds by apoptosis. The host is defined as the larger of the organisms involved in a symbiotic interaction. http://purl.obolibrary.org/obo/go.owl GO:0033669 GO:0052030 activation by organism of host apoptosis activation by organism of host apoptotic programmed cell death induction by organism of host apoptotic programmed cell death induction by symbiont of host apoptosis positive regulation by organism of host apoptotic programmed cell death up regulation by organism of host apoptotic programmed cell death up regulation by symbiont of host apoptosis up-regulation by organism of host apoptotic programmed cell death up-regulation by symbiont of host apoptosis upregulation by organism of host apoptotic programmed cell death upregulation by symbiont of host apoptosis activation by symbiont of host apoptosis positive regulation by symbiont of host apoptosis stimulation by symbiont of host apoptosis biological_process GO:0052151 Note that term is to be used to annotate gene products in the symbiont. To annotate host gene products, consider the biological process term 'positive regulation of apoptosis ; GO:0043065'. positive regulation by symbiont of host apoptotic process Any process in which an organism modulates the frequency, rate or extent of programmed cell death in a second organism, where the two organisms are in a symbiotic interaction. http://purl.obolibrary.org/obo/go.owl GO:0052459 modulation by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction biological_process modulation of programmed cell death in other organism during symbiotic interaction GO:0052248 modulation of programmed cell death in other organism involved in symbiotic interaction Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death by apoptosis in a second organism, where the two organisms are in a symbiotic interaction. http://purl.obolibrary.org/obo/go.owl GO:0052388 induction by organism of apoptosis in other organism involved in symbiotic interaction activation by organism of apoptosis in other organism during symbiotic interaction positive regulation by organism of apoptosis in other organism involved in symbiotic interaction positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction stimulation by organism of apoptosis in other organism during symbiotic interaction biological_process activation by organism of apoptotic programmed cell death in other organism during symbiotic interaction induction by organism of apoptosis in other organism during symbiotic interaction induction by organism of apoptotic programmed cell death in other organism during symbiotic interaction positive regulation by organism of apoptosis in other organism during symbiotic interaction positive regulation by organism of apoptotic programmed cell death in other organism during symbiotic interaction up regulation by organism of apoptosis in other organism during symbiotic interaction up-regulation by organism of apoptosis in other organism during symbiotic interaction upregulation by organism of apoptosis in other organism during symbiotic interaction GO:0052501 positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction Any viral process that activates or increases the frequency, rate or extent of cell death by apoptotic process. http://purl.obolibrary.org/obo/go.owl positive regulation of apoptosis by virus biological_process GO:0060139 positive regulation of apoptotic process by virus Any viral process that modulates the rate or extent of progression through the cell cycle. http://purl.obolibrary.org/obo/go.owl VZ:1636 modulation of host cell cycle by virus regulation by virus of host cell cycle regulation of host cell cycle by virus viral process regulating host cell cycle biological_process GO:0060153 modulation by virus of host cell cycle http://purl.org/obo/owl/gene_ontology biological_process post-mating oviposition Any process that modulates a measurable attribute of any biological process, quality or function. http://purl.obolibrary.org/obo/go.owl regulation biological_process GO:0065007 biological regulation Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc. http://purl.obolibrary.org/obo/go.owl regulation of biological attribute regulation of biological characteristic biological_process GO:0065008 regulation of biological quality http://purl.org/obo/owl/gene_ontology biological_process organism emergence from protective structure measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot unitId measurement unit label objective specification purpose of a study; support of hypothesis, discovery of new information a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take Alan Ruttenberg OBI Plan and Planned Process branch action specification label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO label label software Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI software data item Data items include counts of things, analyte concentrations, and statistical summaries. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item symbol a smallish, word-like datum... 20091104, MC: this needs work and will most probably change PERSON: Jonathan Rees symbol information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity 1 1 10 feet. 3 ml. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. Philippe Rocca-Serra PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI dataSets data set plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum version number A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version GROUP: IAO version number A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg time measurement datum time stamped measurement datum pmid:20604925 - time-lapse live cell microscopy A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. Alan Ruttenberg experimental time series time sampled measurement data set name http://purl.obolibrary.org/obo/MF.owl George Gkoutos 2011-04-14T01:03:39Z "Behaviour related to the activity which primary purpose is the sexual reproduction." [NBO:GVG] behavior_ontology sexual activity Mus musculus William R. Hogan House mouse Mus musculus Virus Poxviridae Chordopoxvirinae Orthopoxvirus Mirela L Vasconcelos monkey pox virus Monkeypox virus Variola virus H5N1 subtype of Influenza A virus H5N1 subtype GC_ID:1 ncbi_taxonomy Herpesviridae GC_ID:1 ncbi_taxonomy Alphaherpesvirinae GC_ID:1 ncbi_taxonomy Simplexvirus HSV-1 HSV1 GC_ID:1 Herpes simplex virus type 1 ncbi_taxonomy Herpes simplex virus 1 Human Herpesvirus-1 Human herpesvirus 1 Human herpesvirus type 1 herpes simplex virus 1 HSV-1 herpes simplex virus HSV-1 herpes simplex virus type 1 HSV-1 herpes simplex virus type 1 HSV1 herpes simplex virus type-1 HSV-1 Human alphaherpesvirus 1 HSV-1 HSV1 Herpes simplex virus type 1 Herpes simplex virus 1 Human Herpesvirus-1 Human herpesvirus 1 Human herpesvirus type 1 herpes simplex virus 1 HSV-1 herpes simplex virus HSV-1 herpes simplex virus type 1 HSV-1 herpes simplex virus type 1 HSV1 herpes simplex virus type-1 HSV-1 HSV2 GC_ID:1 Herpes simplex virus type 2 (HSV-2) ncbi_taxonomy Herpes simplex virus (type 2) Herpes simplex virus 2 Herpes simplex virus II Herpes simplex virus type 2 Human herpesvirus 2 herpes simplex virus type 2 HSV-2 Human alphaherpesvirus 2 HSV2 Herpes simplex virus type 2 (HSV-2) Herpes simplex virus (type 2) Herpes simplex virus 2 Herpes simplex virus II Herpes simplex virus type 2