]> Amanda Hicks William R. Hogan Mike Wagner Matt Diller Josh Hanna John Levander Shawn T. Brown Mathias Brochhausen Apollo Structured Vocabulary (Apollo-SV) 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). https://creativecommons.org/licenses/by/3.0/ v3.0.1 NLM ID National Library of Medicine Identifier This identifier is the one that the National Library of Medicine uses to identify journals uniquely in PubMed. ISSN Linking 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. linking ISSN ISO Title Abbreviation ISO Abbreviations are constructed at NLM to assist NCBI in linking from GenBank to PubMed. Iso Abbr NLM Title Abbreviation The abbreviated journal title assigned by the National Library of Medicine. Typically, it's the ISO title abbreviation without periods. URI creation date The date on which a URI annotated with this property was created. 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. William R. Hogan 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 repository URL 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. WIlliam R. Hogan source code version control 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 hasURL 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. editor preferred term editor preferred term~editor preferred label editor preferred label editor preferred label editor preferred term example of usage example of usage has curation status has curation status definition textual definition textual definition definition definition editor note editor note editor note definition editor term editor definition editor definition editor term editor alternative term alternative term definition source definition source definition source has obsolescence reason curator note curator note imported from OBO foundry unique label elucidation has associated axiom(nl) has associated axiom(fol) ISA alternative term NIAID GSCID-BRC alternative term STATO alternative term Orlaith Burke Alejandra Gonzalez-Beltran Philippe Rocca-Serra an alternative term used for STATO statistical ontology and ISA team external_definition homology_notes Unique Apollo Label UAL 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. has_rank A metadata relation between a class and its taxonomic rank (eg species, family) 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 ncbi_taxonomy Creator Source Source has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym in_subset shorthand label basis of true obsolete is based on 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. commissions commissions A relation between two entities where the first entity formally requests a third party to create or execute the second entity. 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. instantiates 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. simulates 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. causally_precedes true Mathias Brochhausen obsoleted_administrated by true has basis in (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 quality is realized by GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm] executed_during has_realization http://purl.obolibrary.org/obo/obi.owl is_realized_as replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by' obsolete_is_realized_by realized by realized_by realizes realizes preceded by http://purl.obolibrary.org/obo/ro.owl 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. http://www.obofoundry.org/ro/#OBO_REL:preceded_by is preceded by preceded by 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. precedes http://purl.obolibrary.org/obo/ro.owl 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. occurs in unfolds_in Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte http://purl.obolibrary.org/obo/ido.owl http://purl.obolibrary.org/obo/obi.owl occurs_in relationship contains process http://purl.obolibrary.org/obo/bfo.owl [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 containsProcess contains-process is aggregate of http://purl.obolibrary.org/obo/obi.owl aggregate of aggregate_of is aggregate of exists at has material basis at all times http://purl.obolibrary.org/obo/bfo.owl 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)'. has-material-basis_at hasMaterialBasisAt (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] 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]) 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. has occurrent part http://purl.obolibrary.org/obo/bfo.owl [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'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) [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. o-has-part (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) hasOccurrentPart [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match. has proper occurrent part http://purl.obolibrary.org/obo/bfo.owl b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001 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]) has temporal part http://purl.obolibrary.org/obo/bfo.owl [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'] 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]) [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'] 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 has-t-part part of occurrent http://purl.obolibrary.org/obo/bfo.owl [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]) BFO2 Reference: occurrent occurrentPartOf o-part-of (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) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] (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] 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. 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. 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]) the first set of the tennis match occurrent_part_of the tennis match. proper temporal part of http://purl.obolibrary.org/obo/bfo.owl properTemporalPartOf t-ppart-of proper part of occurrent http://purl.obolibrary.org/obo/bfo.owl [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]) properOccurrentPartOf o-ppart-of (iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001] temporal part of http://purl.obolibrary.org/obo/bfo.owl (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001] (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] temporalPartOf t-part-of (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] 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]) 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]) 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 occupies temporal region http://purl.obolibrary.org/obo/bfo.owl spans occupiesTemporalRegion 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 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]) span-of spanOf during which exists specifically depends on at some time BFO2 Reference: specifically dependent continuant\; process; process boundary (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] (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] 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) (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 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 z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002] A pain s-depends_on the organism that is experiencing the pain 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. 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]) 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 a gait s-depends_on the walking object. (All at some specific time.) 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]) 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 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 reciprocal s-dependence between occurrents: a process of buying and the associated process of selling specificallyDependsOn 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 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 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 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 has proper temporal part http://purl.obolibrary.org/obo/bfo.owl has-t-ppart history of has history has measurement unit label is about is duration of Person:Alan Ruttenberg relates a process to a time-measurement-datum that represents the duration of the process has time stamp Alan Ruttenberg relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken has measurement datum Alan Ruttenberg relates a time stamped measurement datum to the measurement datum that was measured true true true achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' BP, AR, PPPB branch PPPB branch derived 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. achieves_planned_objective http://purl.obolibrary.org/obo/obi.owl modified according to email thread from 1/23/09 in accordince with DT and PPPB branch owns http://purl.obolibrary.org/obo/omrse.owl Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal. is owned by http://purl.obolibrary.org/obo/omrse.owl Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. 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. is enrolled in school http://purl.obolibrary.org/obo/omrse.owl is admitted to hospital http://purl.obolibrary.org/obo/omrse.owl is bearer of http://purl.obolibrary.org/obo/omrse.owl bearer of bearer_of has_participant has_participant is_concretization_of immediately_preceded_by 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 X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) directly preceded by http://purl.obolibrary.org/obo/uberon.owl http://semanticscience.org/resource/SIO_000251 immediately_preceded_by immediately_preceded_by is directly preceded by is immediately preceded by starts_at_end_of uberon immediately_precedes ends during 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). negatively regulates http://purl.obolibrary.org/obo/ro.owl Chris Mungall x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y negatively regulates (process to process) has active participant http://purl.obolibrary.org/obo/ro.owl 'heart development' has active participant some Shh protein has agent x has participant y if and only if x realizes some active role that inheres in y Chris Mungall This may be obsoleted and replaced by the original 'has agent' relation temporal relation temporally related to http://purl.obolibrary.org/obo/obi.owl move to BFO? Allen A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. starts with http://purl.obolibrary.org/obo/obi.owl Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor started by 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. ends http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl inverse of ends with ends with finished with http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl 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. causally downstream of http://purl.obolibrary.org/obo/ro.owl inverse of upstream of Chris Mungall causally upstream of http://purl.obolibrary.org/obo/ro.owl Chris Mungall p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain causal relation between processes http://purl.obolibrary.org/obo/ro.owl Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall 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. obsolete has_disposition http://purl.obolibrary.org/obo/ido.owl true relationship negatively_regulates http://purl.obolibrary.org/obo/ido.owl true relationship obsolete_realized_by NOTE: there appears to be some consistency in usage as to whether processes or continuants realize http://purl.obolibrary.org/obo/ido.owl true OBO_REL:0000035 relationship OBO_REL:realized_as regulates http://purl.obolibrary.org/obo/ido.owl true relationship ObsoleteProperty true obsolete has proper part true true true true A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl 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. is expressed as has measurement value Aedes albopictus forest day mosquito Stegomyia albopicta purely intentional entity 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. Johansson I. (2009) Proof of the existence of universals – and Roman Ingarden's Ontology. Metaphysica. International Journal for Ontology & Metaphysics. 10, 65-87 Ingarden, R. (1964) Der Streit um die Existenz der Welt I. Existentalontologie. Max Niemeyer, Tübingen. Ingarden, R. (1965b) Der Streit um die Existenz der Welt II/1. Formalontologie 1. Teil. Max Niemeyer, Tübingen. Ingarden, R. (1965a) Das literarische Kunstwerk. 3. Auflage. Max Niemeyer, Tübingen. 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'. 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. epidemic model William Hogan and Michael Wagner A disease transmission model whose concretization is realized as a simulation of infectious disease epidemic or infectious disease pandemic. An algorithm the concretizations of which models the transmission of transmissible disease. basic reproduction number 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. The average number of transmissions of an infectious agent from an infectious organism to a susceptible organism within a completely susceptible population. The number of organisms that each infected organism infects in a completely susceptible population during its infectious period. William R. Hogan population immunity survey A population survey that assesses the level of immunity against a particular pathogen in a specified population. 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. Mathias Brochhausen simulating of process of type X simulating of process of type X A process that replaces the essential participants of another type of process with representations of those participants. 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. 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. simulation requester identifier 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 software simulator http://en.wikipedia.org/wiki/Simulation_software A software that provides a model of a real phenomenon based on a set of mathematical formulas. A software that provides a model of a real phenomenon based on a set of mathematical formulas. software development A planned process resulting in a software product involving the creation of source code. A planned process resulting in a software product involving the creation of source code. http://en.wikipedia.org/wiki/Software_development simulator developer identifier 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 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. control strategy reactive start time information true A control strategy start time information item that is based on a condition that triggers the control strategy. A control strategy start time information item that is based on a condition that triggers the control strategy. Mathias Brochhausen simulation time step value numberOfUnitsOfTimeInOneSimulatorStep 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. A numeral that is part of a simulation time step action specification. simulator version identifier An identifier that refers to a unique version of a simulator. Simulator version distinguishes, for example, version “2.0” from “2.0.b” An identifier that, as part of a complete simulator identifier, refers to one specific version of a simulator software. simulation time step unit unitOfTimeForSimulatorTimeStep 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”. simulation run length runLength 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. infectious period duration infectiousPeriodDuration A duration of the parts of an infection during which the host bears an infectious disposition in a population of hosts. 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. MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs. Mathias Brochhausen latent period duration latentPeriodDuration MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs Mathias Brochhausen 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. 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. The duration of the period between when an organism becomes infected and when it becomes infectious. 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 Mathias Brochhausen count of simulated population Mathias Brochhausen 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’ The count of (simulated organisms) in a simulated population. The number of simulated organisms in a simulated population. The number does not have to be an integer. vaccination dose schedule A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism. An action specification comprising the number of doses and their timing for a vaccination of an individual organism against a specific infectious agent. vaccination compliance 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. The fraction expressing the probability that an organism who is eligible according to a particular vaccination policy will be consented for that vaccination. vaccination efficacy 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 The degree to which a particular vaccination reduces the probability that a vaccinated individual will have a particular vaccination preventable outcome. The infectious disease treatment efficacy of a vaccine. 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. facility survey A planned process involving counting numbers of facilities in a specific region. A planned process involving counting numbers of facilities in a specific region. school facility census Mathias Brochhausen Motivating use case is Synthia synthetic population data. infectious disease control strategy execution 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. hospital patient population 1 Key motivating use case was Synthia synthetic population data. Mathias Brochhausen simulated population simulation of population simulatorReferencablePopulation 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) 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. count count A measurement datum that is the output of counting. A measurement datum that is the output of counting. Mathias Brochhausen counting Mathias Brochhausen http://en.wikipedia.org/wiki/Counting The planned process of finding the number of elements in a finite set of objects. The planned process of finding the number of elements in a finite set of objects. simulation of organism a simulation that is about an organism normal distribution NormalDistribution 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 simulation of exposed organism 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. A simulation of an infectious agent host that is not contagious and is part of a simulated population. simulated population location identifier An identifier referring to geographical location of a simulated population. Our intent is for the location identifiers to be INCITS codes. Mathias Brochhausen An identifier that refers to a geographical location to be used as location of a population in a simulation. simulation of infectious organism 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. A simulation of an infectious organism host that is contagious. simulation of recovered organism 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. A simulated organism in a simulated population that is not susceptible. simulation of disease disease 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. reproduction number ReproductionNumber Mathias Brochhausen The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection. The number of susceptible organisms that each infected organism infects. ‘Infects’ carries the same meaning as ‘exposes’ in epidemic simulations such as SEIR simulation. nursery school student population 1 Key motivating use case was Synthia synthetic population data. Mathias Brochhausen obsolete_asymptomatic infection fraction asymptomatic infection fraction true 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. vaccine supply schedule 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. vaccination administration capacity 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. antiviral treatment efficacy 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… 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. The infectious disease treatment efficacy of an antiviral drug. antiviral efficacy delay 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. 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. antiviral compliance 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 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 supply schedule 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 administration 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. simulation of organism awaiting control measure A simulated organism in a simulated population that is “eligible, willing and able” to participate with a particular simulated control measure. A simulated organism that is assumed “eligible, willing and able” to participate with a particular 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. complete simulator identifier Mathias Brochhausen An identifier that refers to a specific simulator. 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? 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. epidemic simulating epidemic simulation Mathias Brochhausen A simulating of a disease epidemic or pandemic. the process of simulating a disease epidemic or pandemic. This term is not currently used in Apollo-WS. hospital patient population census 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). simulation of organism not awaiting control measure A simulated organism in a simulated population that is “ineligible, unwilling or unable” to participate with a particular simulated control measure. A simulated organism that is assumed “ineligible, unwilling or unable” to participate with a particular 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 awaiting effect of 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 antiviral control measure 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. 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. The simulation of an antiviral control measure. simulation of vaccination control measure simulation of vaccination 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. primary school student population 1 Key motivating use case was Synthia synthetic population data. simulation of control measure participant A simulated organism in a simulated population has participated in a particular simulated control measure. (e.g. an organism received antiviral treatment) A simulation of an organism in a simulated population that has participated in an epidemic control measure. simulation time series A sequence of data points, where the position in the sequence of each data point corresponds to a specific time_step of the simulation. 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. 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 identifier numeral A numeral that indexes a specific simulation. Class was originally created to correspond with an element from Apollo XSD v3.1.0. 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. simulation of time step simulation time step 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 action specification An action specification that specifies the length of the time steps interval assumed in a simulation. An action specification that specifies the length of the time steps interval assumed in a simulation. Mathias Brochhausen simulation time step value simulation time step unit simulation run length time step identifying numeral simulatorTime A numeral that indexes a specific time step of a simulation. The time step number of a simulation. simulation simulation A purely intentional entity that simulates an entity and its properties. A purely intentional entity that simulates an entity and its properties. obsolete_simulation of population location simulated population location true An identifier referring to geographical location of a simulated population. Our intent is for the location identifiers to be INCITS codes. The simulation of geographical location in which a population is assumed to be located. simulation of susceptible organism A simulated organism in a simulated population that is capable of acquiring a particular simulated disease. A simulation of a susceptible organism in a simulated population. simulation of symptomatic organism A simulated organism in a simulated population that has at least one symptom caused by a particular simulated disease. A simulation of a symptomatic infectious agent host. simulation of asymptomatic organism A simulated organism in a simulated population that has no symptoms caused by a particular simulated disease. A simulation of an asymptomatic infectious agent host. infectious disease control objective specification 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 μ true μ the mean or expectation of a distribution σ sigma standard deviation beta distribution beta distribution 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 deprecated log normal distribution true 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 uniform distribution UniformDistribution A continous probability distribution whose parameters a and b, denote its minimum and maximum values triangular distribution triangular distribution a continuous probability distribution with lower limit a, upper limit b and mode c, where a < b and a <= c <= b. Bayesian network BayesianNetwork a discrete probability distribution temporal Bayesian network temporal Bayesian network a discrete probability distribution that conditions on time control strategy dose schedule 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. 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. age data in age brackets data set 1 A data set consisting of measurements of age organized in age brackets. A data set consisting of measurements of age organized in age brackets. infectious disease control strategy InfectiousDiseaseControlMeasure 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. The essential goal of an infectious disease control strategy is to protect the susceptible organisms in a population. count of susceptible population The count of individuals in a susceptible population (empirical or virtual). The count of individuals in a susceptible population (empirical or virtual). count of contacted population The count of individuals in an exposed population (empirical or virtual). The count of individuals in an exposed population (empirical or virtual). measured vaccination efficacy 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. 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. vaccination efficacy study design execution VaccinationEfficacyStudy 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 obsolete_immune immune true an organism that has the property of being immune to a specific disease agent 95% confidence interval 95% confidence interval 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% Bayesian credible interval Baysesian credible 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. community community 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. William R. Hogan deprecated discrete probability distribution discrete probability distribution true a probability distribution over a discrete random variable obsolete unit of measure true The increments of measurement for a measurable thing ecosystem Ecosystem The sum of all biotic and abiotic entities in a geographical region. The sum of all biotic and abiotic entities in a geographical region. William R. Hogan count of contagious population The count of individuals in a contagious population (empirical or virtual). The count of individuals in a contagious population (empirical or virtual). count of resistant population The count of individuals in a resistant population (empirical or virtual). The count of individuals in a resistant population (empirical or virtual). abiotic ecosystem AbioticEcosystem 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. William R. Hogan fixed control strategy start time specification FixedStartTime 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. control strategy reactive endpoint fraction controlStrategyReactiveEndpointFraction 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. 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. biotic ecosystem BioticEcosystem 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. William R. Hogan software developer identifier softwareDeveloper 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. complete software identifier 1 SoftwareIdentification An identifier that refers to a specific piece of software. An identifier that refers to a specific piece of software. atmosphere William R. Hogan 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 atmosphere of Earth, Earth's moon, Saturn, Titan, etc. outer, gaseous layers of exoplanets are called extraterrestrial atmosphere. software version identifier softwareVersion 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. software identifier softwareName An identifier that refers to all version of a specific software. An identifier that refers to all version of a specific software. atmosphere of geographical region obsolete_educational institution true 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. 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) school closure target facilities 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. infection A process of reproduction of a particular pathogen species inside some tissue of a particular host species. A reproduction of a pathogen organism of a particular biological taxon in a tissue of a host organism from another taxon. M. Brochhausen William R. Hogan 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 process process of infection infection acquisition InfectionAcquisition 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. 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 Mathias Brochhausen 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 vaccine identifier vaccineOntologyId A unique identifier for a vaccine. An identifier that refers to a type of vaccine, i.e., one of a class of manufactured vaccines that public health would consider interchangable. latent period Mathias Brochhausen vaccination identifier 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 course the number of doses of vaccine that are recommended to achieve immunity species species an interbreeding population antiviral identifier antiviralId a unique identifier that refers to an antiviral drug product A unique identifier for an antiviral drug school closure control strategy SchoolClosureControlStrategy A control measure in which schools are closed in an attempt to reduce transmission of disease. A place closure control strategy whose action specification is realized in a school closure process. school closure duration school closure duration The number of time steps that a school closure control measure prescribes that schools will remain closed. school calendar true The time steps that a school will be in session. control strategy target facilities control strategy target facilities Faciilities that are the target of a control strategy control strategy target populations and prioritization ControlMeasureTargetPopulationsAndPrioritization A simulated population that is the target of a control strategy and its priority under triage conditions control strategy target population fraction 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. Fraction of organisms in a target population that a control strategy program seeks to enroll or prioritize obsolete_Reactive control measure Reactive control measure true 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) an epidemic control measure plan specification that has a conditional specification as part reactive control strategy test reactiveControlMeasureTest An event in the ecosystem that triggers the starting or stopping of a control strategy. reactive control strategy threshold reactiveControlMeasureThreshold 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. secondary school student population 1 Key motivating use case was Synthia synthetic population data. control strategy response delay controlMeasureResponseDelay 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. ascertainment 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 fraction fractionInState Fraction of all symptomatic individuals who will be ascertained fraction of organisms (usually infected) that a surveillance system detects out of the total population vaccination control strategy 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. An individual treatment control strategy that has as part an action specification that is realized in a vaccination process. vaccine valence valence the number of distinct antigenic strains in a vaccine product antiviral course 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 control strategy compliance compliance A fraction of eligible individuals in a population who receive an intervention or participate in a control strategy. A measurement datum about the fraction of individuals in a population that elect to participate in a control strategy when offered. 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 infectious period Mathias Brochhausen protect against effect of pathogen Mathias Brochhausen vaccination 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. 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 vaccine disposition true Mathias Brochhausen replaced with VO 'vaccine function' disposition to become contaminated with a pathogen Mathias Brochhausen resistance to infection Mathias Brochhausen 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 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 William R. Hogan beta true 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 inter-personal contact probability inter-personal contact probability Transmission parameter random number seed true random number seed susceptibility measurement datum A number between 0 and 1 indicating the degree of susceptibility of an organism vaccination reactive end point fraction a fraction of the target population, that once vaccinated, results in stopping further vaccination in the population immune resistance to infection Mathias Brochhausen Resistance to infection that is conferred by immune system/immune mechansisms. Resistance to infection that is conferred by immune system/immune mechansisms. population survey A planned process involving counting numbers of a organism population, possibly including counting sub-populations fulfilling specific criteria. A planned process involving counting numbers of a organism population, possibly including counting sub-populations fulfilling specific criteria. Mathias Brochhausen population census The outcome of a population survey. The outcome of a population survey. exposed population exposed population A population of host organisms undergoing infection and that are not infectious. A population of host organisms undergoing infection and that are not infectious. population infection survey PopulationInfectionSurvey A population survey that counts the number of individuals in the population who are infected with a particular pathogen. A population survey that counts the number of individuals in the population who are infected with a particular pathogen. 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'))))) Mathias Brochhausen contagious population A population of host organisms undergoing infection that are contagious. A population of host organisms undergoing infection that are contagious. population infection and immunity census PopulationInfectionAndImmunityCensus 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. A data set that is the result of a population infection survey and a population immunity survey. Mathias Brochhausen PII Census population demographic survey population demographic census A data set that is the specific outcome of a population demographic survey. A data set that is the specific outcome of a population demographic survey. Mathias Brochhausen obsolete_contamination true Mathias Brochhausen MIDAS scenario true An ecosystem in which a population of hosts is undergoing at least one infection. An ecosystem in which a population of hosts is undergoing at least one infection. Mathias Brochhausen MIDAS scenario representation An information content entity that is about a MIDAS scenario and contains population disease census data. An information content entity that is about a MIDAS scenario and contains population disease census data. Mathias Brochhausen need to change the text definition. need to change label to be more consistent with current Apollo terminology (possibly 'infectious disease scenario'. recovered population 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 agent-level ecosystem data generation William R. Hogan Matthew Diller A planned process that has one or more synthetic ecosystem datasets as output. A planned process that has one or more synthetic ecosystem datasets as output. Mathias Brochhausen creating a synthetic ecosystem dataset synthetic ecosystem constructing synthetic ecosystem generating agent-level ecosystem census A data set that is the specified output of a agent-level ecosystem data generation that had census data as an input. A data set that is the specified output of a agent-level ecosystem data generation that had census data as an input. Mathias Brochhausen contaminated thing 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. An independent continuant that is the localization of a pathogen, but is not undergoing an infection. An independent continuant that is the localization of a pathogen, but is not undergoing an infection. Mathias Brochhausen contamination acquisition ContaminationAcquisition 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. 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 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 Motivating use case is Synthia synthetic population data. antiviral treatment AntiviralTreatment A treatment of a particular host with a particular antiviral drug with activity against a particular viral pathogen. A treatment with an antiviral drug. susceptibility Mathias Brochhausen The ability to participate in infection acquisition as a host. The ability to participate in infection acquisition as a host. census CensusData Mathias Brochhausen The count of a specific entity in a specified region at a specified time. The count of a specific entity in a specified region at a specified time. disease transmission model disease transmission model 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. obsolete_school organization true An organization created with the purpose of providing education to those of its members that are bearer of student role. An organization created with the purpose of providing education to those of its members that are bearer of student role. Mathias Brochhausen school student population census Mathias Brochhausen Motivating use case is Synthia synthetic population data. school student population 1 Key motivating use case was Synthia synthetic population data. Mathias Brochhausen The collection of students administrated by exaclty one school organization. The collection of students administrated by exaclty one school organization. simulator configuration simulatorConfiguration 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. obsolete_student role true A human social role that is realized by attending a school to receive formal education. A human social role that is realized by attending a school to receive formal education. Mathias Brochhausen antiviral control strategy An anti-infective individual treatment control strategy that has as part an action specification that is realized in antiviral treatment. 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. Mathias Brochhausen contagiousness simulator time specification SimulatorTimeSpecification 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). infectious disease scenario InfectiousDiseaseScenario 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. 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. Data about an infection in an ecosystem at a specific location and point in time. William R. Hogan scenario date scenarioDate A reference to the date that corresponds to simulator time zero. An information content entity that refers to a real date corresponding to simulator time zero. contamination 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. 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 biological 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. population treatment census PopulationTreatmentCensus 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. population and environment 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. control strategy inventory 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. contagious organism infectious 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. transmission coefficient beta 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. obsolete vaccination efficacy measured true A data item specifying a measured vaccination efficacy. A data item specifying a measured vaccination efficacy. vaccination efficacy inferred VaccinationEfficacyInferred A data item inferring a vaccination efficacy based on epidemiological data. A data item inferring a vaccination efficacy based on epidemiological data. individual treatment control strategy IndividualTreatmentControlMeasure An infectious disease control strategy that immediately targets individuals. An infectious disease control strategy that immediately targets individuals. Mathias Brochhausen vaccination control strategy, antiviral control strategy target population TargetPopulation An organism population that is the target for a disease control strategy. An organism population that is the target for a disease control strategy. ring vaccination individual treatment control strategy agent level population and environment census 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 model ecosystem census description true 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. compartment model population and environment census 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). population strata definition PopulationStrataDefinition contaminated thing census ContaminatedThingCensus 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. indexable Apollo item 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. NCBI taxon identifier An identifier curated by the National Center for Biotechnology Information (NCBI) that designates a particular biological taxon (e.g., Homo sapiens). NcbiTaxonId An identifier curated by the NCBI Taxonomy that designates a biological taxon. disease outcome diseaseOutcome A processual entity that is either the outcome of a disease course or a part of a disease course and has etiological relevance. An event that happens during the course of a disease and that results from pathological processes that happened earlier in the disease. 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), William R. Hogan susceptible organism susceptible An organism of a particular species that can undergo infection with a particular pathogen. An organism that is the bearer of a susceptibility disposition. William R. Hogan immune organism immune An organism of a particular species that has developed immune resistance to infection with a pathogen of a particular species. An organism that is the bearer of an immune resistance disposition. William R. Hogan resistant organism resistant An organism of a particular species that is unable to undergo infection with a particular pathogen. William R. Hogan an organism that is the bearer of resistance to infection control strategy start time information controlMeasureStartTime A specification of when an infectious disease control strategy starts. An information content entity that specifies the start time of the implementation of a infectious disease control strategy. infected organism infected 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. An infectious agent host who is NOT able to transmit the infection to another organism of the same species. William R. Hogan organism in latent period of infection apollo simulator configuration RunSimulationMessage A simulator configuration that start an Apollo simulator. A simulator configuration that start an Apollo simulator. Mathias Brochhausen transmission probability TransmissionProbability 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. treatment administration capacity schedule capacitySchedule 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. treatment supply schedule supplySchedulePerDay A schedule that specifies the availability of a particular drug over a specific temporal interval in a specified geographical region. 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. Mathias Brochhausen vaccination efficacy for simulator configuration VaccinationEfficacyForSimulatorConfiguration An information content entity that specifies the vaccination efficacy that is part of a simulator configuration. An information content entity that specifies the vaccination efficacy that is part of a simulator configuration. Mathias Brochhausen probability distribution ProbabilityDistribution 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. 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 discrete probability distribution a probability distribution over a discrete random variable a probability distribution over a discrete random variable infection state data item infectionState 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. 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 vaccination preventable outcome vaccinationPreventableOutcome An objective specification that specifies the disease outcome a vaccination seeks to prevent. An objective specification that specifies the disease outcome a vaccination seeks to prevent. Mathias Brochhausen Apollo pathogen code ApolloPathogenCode 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. An information content entity that designates a biological taxon and optionally a clade of pathogens. Mathias Brochhausen abiotic ecosystem element A material entity that is part of an abiotic ecosystem. 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. Mathias Brochhausen immune population acting like immune An immune population that acts as the members know they are immune (do not seek vaccination/antiviral treatment, etc.). An immune population that acts as the members know they are immune (do not seek vaccination/antiviral treatment, etc.). Mathias Brochhausen immune population acting like not immune An immune population that acts as the members assume they are not immune (e.g. seek vaccination/antiviral treatment). An immune population that acts as the members assume they are not immune (e.g. seek vaccination/antiviral treatment). Mathias Brochhausen becoming asymptomatic asymptomatic Mathias Brochhausen The process of an organism stopping to experience any symptoms caused by a disease. The process of an organism stopping to experience any symptoms caused by a disease. becoming symptomatic symptomatic Mathias Brochhausen The process of an organism beginning to experience symptoms caused by a disease. The process of an organism beginning to experience symptoms caused by a disease. becoming severely symptomatic severely symptomatic Mathias Brochhausen The process of an organism beginning to experience severe symptoms caused by a disease. The process of an organism beginning to experience severe symptoms caused by a disease. infectiousness profile infectiousnessProfile A process profile that specifies the degree to which a host is likely to pass on an infection to a susceptible organism. A process profile that specifies the degree to which a host is likely to pass on an infection to a susceptible organism. Mathias Brochhausen This is probably a 'process profile' according to BFO2 infectious disease treatment efficacy TreatmentEfficacy 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. 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 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. border control strategy BorderControlMeasure A travel-related infectious disease control strategy that has an action specification that is realized in restricting movement of organisms across international borders. 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 place closure control strategy PlaceClosureControlMeasure 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. 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. case isolation control strategy CaseQuarantineControlMeasure 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. William R. Hogan an infectious disease control strategy that has an action specification that is realized in isolating organsims who are infectious. travel restriction control strategy TravelRestrictionControlMeasure A travel-related infectious disease control strategy whose action specification is realized in restricting travel of organims from one ecosystem to another ecosystem A travel-related infectious disease control strategy whose action specification is realized in restricting travel of organims from one geographical region to another William R. Hogan clade name cladeName A reference to a group or groups of organisms that are based on common ancestry. An identifier that denotes a group of organisms or groups of organisms based on common ancestors. Mathias Brochhausen Some regard a clade to be a single branch on the tree of life. [http://en.wikipedia.org/wiki/Clade] infected population A population of only infected members of one species. A population of only infected members of one species. susceptible population A population of organisms that are all susceptible. A population of organisms that are all susceptible. immune population A population of organisms that are all immune. A population of organisms that are all immune. asymptomatic host pathogen pathogen 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. host 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 infectious disease InfectiousDisease 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. 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. census reference date referenceDate A information content entity that specifies the date of a census. A information content entity that specifies the date of a census. Mathias Brochhausen age range category AgeRangeCategoryDefinition An information content entity specifying the upper and lower limit of a range of ages of continuants. An information content entity specifying the upper and lower limit of a range of ages of continuants. Mathias Brochhausen name of temporal interval TimeSpanCategoryDefinition An information content entity that specifies a time span on a specified time scale by giving a start time and a duration. An information content entity that specifies a time span on a specified time scale by giving a start time and a duration. Mathias Brochhausen duration Duration A measurement datum that quantifies a temporal region that is occupied by a processual entity. A measurement datum that quantifies a temporal region that is occupied by a processual entity. Mathias Brochhausen disease identifier A unique identifier that refers to a particular type of disease. Mathias Brochhausen We still need to decide which coding schema to adopt.-MB a unique identifier that refers to a disease. conditional probability distribution ConditionalProbabilityDistribution A probability distribution of two jointly distributed random variables X and Y, where Y is know to be a particular value. A probability distribution of two jointly distributed random variables X and Y, where Y is know to be a particular value. Mathias Brochhausen joint 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. 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 unconditional probability distribution UnconditionalProbabilityDistribution 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. 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 obsolete parametric probability distribution ParametricProbabilityDistribution true Mathias Brochhausen nonparametric probability distribution NonparametricProbabilityDistribution Mathias Brochhausen discrete parametric probability distribution DiscreteParametricProbabilityDistribution Mathias Brochhausen continuous parametric probability distribution ContinuousParametricProbabilityDistribution Mathias Brochhausen discrete nonparametric probability distribution DiscreteNonparametricProbabilityDistribution Mathias Brochhausen continuous nonparametric probability distribution Mathias Brochhausen log normal distribution LogNormalDistribution A continuous parametric probability distribution that takes as its input a normally-distributed logarithmic function with mean μ and standard deviation σ. Mathias Brochhausen a log-normal (or lognormal) distribution is a continuous probability distribution of a random variable whose logarithm is normally distributed. http://en.wikipedia.org/w/index.php?title=Log-normal_distribution&oldid=601643223 gamma distribution GammaDistribution 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 the gamma distribution is a two-parameter family of continuous probability distributions Weibull Distribution WeibullDistribution Mathias Brochhausen The Weibull distribution 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." The Weibull distribution 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." The Weibull distribution 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." continuous uniform distribution ContinuousUniformDistribution 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. 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. delay from symptoms to treatment Mathias Brochhausen The duration between the appearance of symptoms of a disease and the start of a treatment. The duration between the appearance of symptoms of a disease and the start of a treatment. delayFromSymptomsToTreatment apollo location code ApolloLocationCode 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). An identifier that refers to a particular geographical region and that is constructed per guidelines of the Apollo project. William R. Hogan control strategy stop time information controlMeasureStopTime 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. William R. Hogan infectious disease control strategy trigger definition TriggerDefinition 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). A rule that specifies the event that, when it occurs, is the trigger to either start or stop an infectious disease control strategy. William R. Hogan contamination probability 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 control strategy stand-down delay controlMeasureStandDownDelay 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. William R. Hogan infection acquisition from contaminated thing InfectionAcquisitionFromContaminatedAbioticThing An infection acquisition from a contaminated thing. An infection acquisition whereby a susceptible host acquires an infection from a contaminated thing. William R. Hogan infection acquisition from infectious host InfectionAcquisitionFromInfectedHost 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. An infection acquisition whereby a susceptible host acquires an infection from an infectious host. William R. Hogan disease surveillance capability DiseaseSurveillanceCapability A capability associated with a location to detect individuals in a population with a particular type of disease. 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 Specifies location, pathogen, host taxon, caseDefinition, sensitivity, specificity, and time delay of case detection time delay to case detection timeDelayToCaseDetection Mathias Brochhausen The duration from the time an organism satisfies a case definition until a process or system detects the organism as satisfying that case definition 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. time scale name timeScale 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. An identifier that designates a scale according to which time is measured (e.g., Gregorian Calendar). William R. Hogan disease surveillance trigger definition DiseaseSurveillanceTriggerDefinition 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. An infectious disease control trigger definition for a reactive control measure based on the outcome of disease surveillance. Mathias Brochhausen treatment surveillance trigger definition TreatmentSurveillanceTriggerDefinition An infectious disease control trigger definition for a reactive control measure based on the outcome of disease surveillance. An infectious disease control trigger definition for a reactive control measure based on the outcome of disease surveillance. Mathias Brochhausen temporal trigger definition TemporalTriggerDefinition A control strategy trigger that occurs once a constant duration of time has elapsed. An infectious disease control trigger definition that is based on the passage of a specified interval of time. time since time scale zero timeSinceTimeScaleZero A duration of time that has elapsed since the zero reference point of a time scale. William R. Hogan the duration of time that has elapsed from the zero reference point to a later time on the time scale seasonal function parameter SeasonalityFunctionParameters maximum seasonal latitude maximumSeasonalLatitude minimum seasonal latitude minimumSeasonalLatitude seasonal temporal offset seasonalTemporalOffset sensitivity of case detection sensitivityOfCaseDetection The sensitivity of a process or system that detects organisms who satisfy a case definition. 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. probability of entry into a country is denied probabilityEntryDenied An information content entity specifying the probability that entry is denied as part of a border control strategy. An information content entity specifying the probability that entry is denied as part of a border control strategy. Mathias Brochhausen probability of exit from a country is denied probabilityExitDenied An information content entity specifying the probability that exit is denied as part of a border control strategy. An information content entity specifying the probability that exit is denied as part of a border control strategy. Mathias Brochhausen duration of treatment course durationOfTreatmentCourse A duration that measures the temporal interval occupied by a treatment course. A period from the start to the end of a treatment course. Mathias Brochhausen number of doses in a treatment course numDosesInTreatmentCourse Mathias Brochhausen The count of the number of doses that are part of a treatment course. The number of doses (of material such as antiviral drug or vaccine) that constitutes a particular course of treatment target populations and prioritizations information targetPopulationsAndPrioritizations A specification of the target populations of a control strategy and the priority of each population in the strategy. school transmission multiplier schoolTransmissionMultiplier William R. Hogan A factor by which to multiply the transmission coefficient for contacts that occur in in a school. 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 household transmission multiplier householdTransmissionMultiplier Matthew Diller A factor by which to multiply the transmission coefficient for contacts that occur in a household. An epidemic simulator action specification that specifies the factor by which to multiply the transmission coefficient for contacts that occur in a household. William R. Hogan workplace transmission multiplier workplaceTransmissionMultiplier A factor by which to multiply the transmission coefficient for contacts that occur in a workplace. An epidemic simulator action specification that specifies the factor by which to multiply the transmission coefficient for contacts that occur in a workplace. William R. Hogan Matthew Diller close individual places independently strategy closeIndividualPlacesIndependently 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. place closure period closurePeriod A period from the closure of a place until the time when it is reopened. William R. Hogan community transmission multiplier communityTransmissionMultiplier maximum travel distance in km information maximumTravelDistanceInKm treatment preventable outcome TreatmentPreventableOutcome An objective specification that specifies the disease outcome that a treatment seeks to prevent. An objective specification that specifies the disease outcome that a treatment seeks to prevent. William Hogan time delay of treatment detection timeDelayOfTreatmentDetection 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 The duration from treatment until a treatment surveillance system detects it in a population William R. Hogan individual treatment strategy supply schedule unit of measure supplyScheduleUnits The unit of measure for the supply schedule of an individual treatment. The unit of measure for the supply schedule of an individual treatment. For example, 'daily dose'. William R. Hogan individual treatment strategy administration capacity unit of measure The unit of measure for the administration capacity of an individual treatment. For example, 'daily dose'. William R. Hogan administrationCapacityUnits agent-based disease transmission model 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. William R. Hogan reactive control strategy threshold unit of measure unitOfMeasureForThreshold A unit of measure for a threshold in a reactive infectious disease control strategy. A unit of measure for a threshold in a reactive infectious disease control strategy. William R. Hogan case definition CaseDefinition 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. 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 obsolete quarantine period true 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. William R. Hogan epidemic Epidemic 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. 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. 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. William R. Hogan epidemic of infection immune organism that acts like it is immune immuneAndActsLikeImmune An immune organism that acts as if it is immune (i.e., it does not seek vaccination or avoid contact with infectious organisms). 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.) William R. Hogan immune organism that acts like it is not immune immuneButActsLikeNotImmune An immune organism that acts as if it is NOT immune (i.e., it seeks vaccination and/or avoids contact with infectious organisms). 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.) William R. Hogan naturally-acquired active immune resistance 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. 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 recovered organism 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. An organism that is the bearer of a naturally-acquired, active immune resistance to infection. William R. Hogan recovered compartmental disease transmission model 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. anti-infective individual treatment control strategy DrugTreatmentControlStrategy anti-infective control strategy 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. An individual treatment control strategy that has as part an action specification that is realized in anti-infective treatment. William R. Hogan anti-bacterial control strategy An anti-infective individual treatment control strategy that has as part an action specification that is realized in antibacterial treatment. 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. William R. Hogan infection in ecosystem A process comprised of numerous infections and infection acquisitions with a particular pathogen in one or more populations of hosts. A process of ongoing infection and infection acquisition in individuals in one or more populations in an ecosystem. William R. Hogan infection in an ecosystem endemic vector control strategy VectorControlMeasure 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'. An infectious disease control strategy that has a vector control action specification as part. Typically, the strategy is to limit the population of the second host species, which is called the "vector" for the infection. William R. Hogan abiotic ecosystem census AbioticThingCensus A census of entities of a certain type or types in the abiotic ecosystem. A census of things in the abiotic ecosystem. William R. Hogan vector control action specification 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". 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 Breteau Index breteauIndex The average number of containers positive (for presence of mosquito) per 100 households. 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 individual mosquito reproduction MosquitoReproduction A multicellular organism reproduction that has as its agent a mosquito (taxon Culicidae, ID 7157) Reproduction of a single mosquito William R. Hogan gonotrophic cycle duration gonotrophicPeriodDuration A time measurement datum of the length of the temporal interval occupied by a gonotropic period. Matthew Diller The duration of the gonotrophic cycle in a female mosquito. William R. Hogan gonotrophic cycle The process in a female mosquito of taking a blood meal, developing eggs, and laying the eggs (oviposition). The process in a female mosquito of taking a blood meal, developing eggs, and laying the eggs (oviposition). William R. Hogan oviposition site census A census of sites where mosquitoes have laid their eggs. An abiotic ecosystem census of the locations where pregnant female mosquitos lay their eggs. OvipositionSiteCensus William R. Hogan obsolete carrying capacity per house carryingCapacityPerHouse true The maximum number of ovisites in/around a single house or other dwelling structure. William R. Hogan incubation period incubationPeriod 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. The period from onset of infection to onset of symptoms. William R. Hogan drug treatment DrugTreatment A treatment with a drug product. Treatment with a drug. William R. Hogan voluntary household quarantine control strategy VoluntaryHouseholdQuarantineControlMeasure 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. An infectious disease control strategy whereby the household members of infectious indivduals voluntarily stay at home to avoid further potentially infectious contacts. liberal sick leave control strategy LiberalSickLeaveControlMeasure 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. 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. epidemic investigation design A study design that specifies which epidemic(s) to investigate, how, and what information to output. William R. Hogan epidemic investigation study design quarantine control strategy 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. William R. Hogan quarantine control strategy larvicide control strategy LarvicideControlMeasure A vector control strategy that kills larval-stage vector organisms William R. Hogan Matthew Diller A vector control strategy that has an action specification that is realized by reducing the number of larval-stage organisms of a vector population. colonization Colonization Primary use case is colonization of humans, animals with Staph aureus, but it also covers bacteriuria, transient bactermia, and normal gut flora. 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. 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. biological colonization infection in population Infection William R. Hogan an infection in an ecosystem occurring in one population of organisms an infection in an ecosystem occurring in one population of organisms infection in a population colonization acquisition ColonizationAcquisition 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 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 colonization acquisition the host organism was not colonized wtih the pathogen prior to the colonization acquisition decolonization control strategy DecolonizationControlMeasure 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 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 decolonization control strategy typically the pathogen is a bacterium infection acquistion 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. 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 establishment of infection 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. 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 William R. Hogan chemical resistance to infection chemoprotection chemoprotective resistance chemotherapeutic resistance to infection resistance to malaria infection A resistance to infection by P. vivax, P. ovale, P. malariae, and/or P. falciparum. A resistance to infection by P. vivax, P. ovale, P. malariae, and/or P. falciparum. William R. Hogan malaria resistance resistance to malaria resistance to malaria infection ectosymbiosis A symbiosis where the two organisms that are interacting remain physically external to one another. It includes situations where one organism lives on the surface of the other organism. William R. Hogan Matthew Diller A symbiosis where the two organisms that are interacting remain physically external to one another. antagonism Example: competition between lions and hyenas for food William R. Hogan An ectosymbiosis that results in harm to both organisms. An ectosymbiosis that results in harm to both organisms. Matthew Diller amensalism William R. Hogan An ectosymbiosis that results in harm to one of the organisms but neither harms nor benefits the other organism. Matthew Diller An ectosymbiosis that results in harm to one of the organisms but neither harms nor benefits the other organism. Example: Spanish ibex and weevils of the genus Timarcha agonism An ectosymbiosis that results in harm to one of the organisms and benefit to the other organism. An ectosymbiosis that results in harm to one of the organisms and benefit to the other organism. William R. Hogan Matthew Diller intimate agonism William R. Hogan Matthew Diller An agonism where the two organisms, although physically external to one another, nevertheless have close and persistent physical contact for most or all of the interaction. An agonism where the two organisms, although physically external to one another, nevertheless have close and persistent physical contact for most or all of the interaction. ectosymbiotic parasitism Matthew Diller An intimate agonism in which the harm is not fatal to the host. An intimate agonism in which the harm is not fatal to the host. William R. Hogan Example: Temnocephala chilensis and various marine wildlife ectoparasitism facultative ectosymbiotic parasitism William R. Hogan Matthew Diller An ectosymbiotic parasitism that realizes a disposition of the parasite that is not one of its biological functions. 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 ectoparasitism obligatory ectosymbiotic parasitism Matthew Diller An ectosymbiotic parasitism that realizes a biological function of the parasite. An ectosymbiotic parasitism that realizes a biological function of the parasite. Example: European common cuckoo and other bird species (brood parasitism) William R. Hogan obligatory ectoparasitism ectosymbiotic parasitoidism An intimate agonism in which the harm is fatal to the host. William R. Hogan An intimate agonism in which the harm is fatal to the host. Matthew Diller ectoparasitoidism facultative ectosymbiotic parasitoidism An ectosymbiotic parasitoidism that realizes a disposition of the parasitoid that is not one of its biological functions. Example: Pachycrepoideus dubius and Ceratitis capitata Matthew Diller An ectosymbiotic parasitoidism that realizes a disposition of the parasitoid that is not one of its biological functions. William R. Hogan facultative ectoparasitoidism obligatory ectosymbiotic parasitoidism An ectosymbiotic parasitism that realizes a biological function of the parasitoid. Example: Mutillidae (family of wasps) and other wasps/ants William R. Hogan An ectosymbiotic parasitism that realizes a biological function of the parasitoid. Matthew Diller obligatory ectoparasitoidism ectosymbiotic commensalism William R. Hogan Matthew Diller An ectosymbiosis that results in benefit to one organism and neither harm nor benefit to the other organism. An ectosymbiosis that results in benefit to one organism and neither harm nor benefit to the other organism. ectocommensalism facultative ectosymbiotic commensalism An ectosymbiotic commensalism that realizes a dispostion of the organism that benefits that is not one of its biological functions. An ectosymbiotic commensalism that realizes a dispostion of the organism that benefits that is not one of its biological functions. William R. Hogan Example: Ophiodromus pugettensis and Patiria miniata Matthew Diller facultative ectocommensalism obligatory ectosymbiotic commensalism Matthew Diller An ectosymbiotic commensalism that realizes a biological function of the organism that benefits. Example: Basicladia algae and sea turtles William R. Hogan An ectosymbiotic commensalism that realizes a biological function of the organism that benefits. obligatory ectocommensalism ectosymbiotic mutualism Matthew Diller An ectosymbiosis that results in benefit to both organisms. William R. Hogan An ectosymbiosis that results in benefit to both organisms. ectomutualism facultative ectosymbiotic mutualism An ectosymbiotic mutualism that realizes one or more dispositions of one or both organisms and these dispostions are not biological functions of either organism. William R. Hogan Matthew Diller 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 ectomutualism obligatory ectosymbiotic mutualism An ectosymbiotic mutualism that realizes a biological function of at least one of the organisms participating. William R. Hogan An ectosymbiotic mutualism that realizes a biological function of at least one of the organisms participating. Example: bees and flowers Matthew Diller obligatory ectomutualism endosymbiosis A symbiosis where one organism is physically contained within the other organism (called the 'host'). William R. Hogan Matthew Diller A symbiosis where one organism is physically contained within the other organism (called the 'host'). endosymbiotic parasitism An endosymbiosis that results in benefit to the parasite and harm to the host. Matthew Diller William R. Hogan An endosymbiosis that results in benefit to the parasite and harm to the host. endoparasitism non-intimate agonism An agonism where the two organisms maintain significant physical separation from one another through most or all of the interaction. Matthew Diller An agonism where the two organisms maintain significant physical separation from one another through most or all of the interaction. William R. Hogan predation A non-intimate agonism in which the harm is fatal. Example: lion and gazel Matthew Diller William R. Hogan A non-intimate agonism in which the harm is fatal. grazing 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 facultative endosymbiotic parasitism An endosymbiotic parasitism that realizes a disposition of the parasite that is not one of its biological functions. William R. Hogan Matthew Diller 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 endoparasitism obligatory endosymbiotic parasitism Matthew Diller William R. Hogan An endosymbiotic parasitism that realizes a biological function of the parasite. An endosymbiotic parasitism that realizes a biological function of the parasite. Example: Necator americanus (hookworm) and humans obligatory endoparasitism endosymbiotic parasitoidism An endosymbiosis that results in benefit to the parasitoid and is fatal to the host. An endosymbiosis that results in benefit to the parasitoid and is fatal to the host. Matthew Diller William R. Hogan endoparasitoidism facultative endosymbiotic parasitoidism Matthew Diller An endosymbiotic parasitoidism that realizes a disposition of the parasitoid that is not one of its biological functions. 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 William R. Hogan facultative endoparasitoidism obligatory endosymbiotic parasitoidism William R. Hogan An endosymbiotic parasitoidism that realizes a biological function of the parasitoid. An endosymbiotic parasitoidism that realizes a biological function of the parasitoid. Matthew Diller Example: Ichneumon eumerus (wasp) and Phengaris rebeli (butterfly caterpillar) obligatory endoparasitoidism endosymbiotic commensalism William R. Hogan Matthew Diller An endosymbiosis that results in benefit to one organism and neither harm nor benefit to the other organism. An endosymbiosis that results in benefit to one organism and neither harm nor benefit to the other organism. endocommensalism facultative endosymbiotic commensalism An endosymbiotic commensalism that realizes a dispostion of the non-host organism that benefits that is not one of its biological functions. William R. Hogan Matthew Diller 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 endocommensalism obligatory endosymbiotic commensalism An ectosymbiotic commensalism that realizes a biological function of the non-host organism that benefits. An ectosymbiotic commensalism that realizes a biological function of the non-host organism that benefits. Example: Passalurus ambiguus (nematode) and rabbits Matthew Diller William R. Hogan obligatory endocommensalism endosymbiotic mutualism William R. Hogan Matthew Diller An endosymbiosis that results in benefit to both organisms. An endosymbiosis that results in benefit to both organisms. endomutualism facultative endosymbiotic mutualism Matthew Diller An endosymbiotic mutualism that realizes one or more dispositions of one or both organisms and these dispostions are not biological functions of either organism. 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 William R. Hogan facultative endomutualism obligatory endosymbiotic mutualism An endosymbiotic mutualism that realizes a biological function of at least one of the organisms participating. Matthew Diller William R. Hogan An endosymbiotic mutualism that realizes a biological function of at least one of the organisms participating. Example: marine worms of genus Riftia and their endosymbiotic bacteria obligatory endomutualism homeostasis 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. 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. William R. Hogan Matthew Diller bodily harm 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 benefit 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. 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 parasite Matthew Diller An organism participating in an ectosymbiotic or endosymbiotic parasitism as the organism that benefits. An organism participating in an ectosymbiotic or endosymbiotic parasitism as the organism that benefits. William R. Hogan parasitoid An organism participating in an ectosymbiotic or endosymbiotic parasitoidism as the organism that benefits. William R. Hogan An organism participating in an ectosymbiotic or endosymbiotic parasitoidism as the organism that benefits. Matthew Diller target population definition TargetPopulationDefinition 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. name of a temporal boundary RealTimePointCategoryDefinition William R. Hogan An information content entity that designates a temporal boundary An information content entity that designates a temporal boundary Matthew Diller location definition LocationDefinition Matthew Diller 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. 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. treatment contraindication TreatmentContraindication A contraindication that increases the risk of a treatment. William R. Hogan Matthew Diller A contraindication that increases the risk of a treatment. uncertain duration UncertainDuration A duration that is specified as a probability distribution over a range of numbers. A duration that is specified as a probability distribution over a range of numbers. Matthew Diller William R. Hogan fraction of contaminated thing fractionContaminated 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. William R. Hogan Matthew Diller 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. specificity of case detection specificityOfCaseDetection 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. The specificity of a process or system that detects organisms who satisfy a case definition. William R. Hogan specificity of case detection specificity of treatment detection specificityOfTreatmentDetection 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. The specificity of the process or system that detects organisms that have undergone a particular treatment. William R. Hogan sensitivity of treatment detection sensitivityOfTreatmentDetection 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. The sensitivity of the process or system that detects organisms that have undergone a particular treatment. William R. Hogan fixed duration FixedDuration A duration that is specified as a single number. A duration that is specified as a single number. real time span category definition RealTimeSpanCategoryDefinition real date span category definition RealDateSpanCategoryDefinition census objective specification 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. William R. Hogan Matthew Diller 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 plan specification A plan specification with a census objective specification. A plan specification with a census objective specification. William R. Hogan Matthew Diller census taking Census A planned process that realizes a census plan specification. William R. Hogan Matthew Diller A planned process that realizes a census plan specification. Wolbachia vector control strategy WolbachiaControlStrategy 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. 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 indoor residual spraying vector control strategy IndoorResidualSprayingVectorControlMeasure 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. A vector control strategy that is realized by spraying chemicals in a place to kill individuals of the vector population. container reduction vector control strategy ContainerReductionControlMeasure A vector control strategy for mosquitoes that is realized by reducing the number of water-containing vessels in which mosquitoes can lay eggs. 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. Matthew Diller treatment system logistics TreatmentSystemLogistics 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. 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. treatment surveillance capability TreatmentSurveillanceCapability 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. 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 name of temporal region population serology survey PopulationSerologySurvey A population survey that assesses the presence (plus or minus quantity) of antibody to a particular antigen in individuals in a population. 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 infection case list CaseList William R. Hogan A data set that is a collection of case records. A data set that is a collection of case records. Matthew Diller infection case record CaseRecord Matthew Diller 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. 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. William R. Hogan deprecated infection case count true A count of individuals in a population who meet an infection case definition during a particular time interval. William R. Hogan Matthew Diller A count of individuals in a population who meet an infection case definition during a particular time interval. epidemic interval EpidemicPeriod Matthew Diller The temporal interval occupied by an epidemic. The temporal interval occupied by an epidemic. epidemic period individual mosquito behavior MosquitoBehavior Matthew Diller An individual behavior of a mosquito (organism of family Culicidae). An individual behavior of a mosquito (organism of family Culicidae). William R. Hogan individual human behavior HumanBehavior Matthew Diller William R. Hogan An individual behavior of a human being. An individual behavior of a human being. transmission tree TransmissionTree 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. William R. Hogan Matthew Diller 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. 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. infectiousness 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. 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.). William R. Hogan infectious disposition potentially infectious contacting 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. 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 potentially infectious contact process potentially infectious contact role A role borne by an organism that is realized in a potentially infectious contact process. 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. William R. Hogan contact role infectious contact role potentially infectous contact role contacted organism An organism that has been exposed to a pathogen by coming into close physical proximity with either an infectious host or a contaminated thing. An organism that is the bearer of a potentially infectious contact role during a potentially infectious contact process. William R. Hogan potentially infectious contact organism contact definition ContactDefinition 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. 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 potentially infectious contact definition ring individual treatment control strategy RingIndividualTreatmentControlMeasure 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. Wolbachia release site wolbachiaReleaseSites A seed site for a Wolbachia control measure. A site that is the bearer of a role which is realized by the release of Wolbachia-infected mosquitos. Matthew Diller William R. Hogan Wolbachia every nth site release action specification wolbachiaSitesEveryNth William R. Hogan Matthew Diller A vector control action specification that specifies the location of Wolbachia release sites according to some predetermined spatial interval. A vector release site action specification for a Wolbachia control measure. leakage rate of Wolbachia infection in mosquito population infected with Wolbachia wolbachiaEffectOnLeakageRate Matthew Diller The rate at which offspring of the Wolbachia-infected female mosquito subpopulation (of the overall mosquito population) are not infected with Wolbachia. The rate at which offspring of the Wolbachia-infected female mosquito subpopulation (of the overall mosquito population) are not infected with Wolbachia. William R. Hogan transmission rate of pathogen to human from Wolbachia-infected mosquito bites wolbachiaEffectOnVectorialCapacity 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. 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. adult vector control strategy William R. Hogan Matthew Diller A vector control strategy that is realized by reducing the number of adults in a vector population. A vector control strategy that is realized by reducing the number of adults in a vector population. Wolbachia prerelease adult vector control strategy wolbachiaPreReleaseAdultSuppressionEfficacy 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. 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. Wolbachia prerelease larvicide vector control strategy wolbachiaPreReleaseLarvalSuppressionEfficacy 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. William R. Hogan Matthew Diller 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. life stages with duration and mortality LifeStageWithDurationAndMortality 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. 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. William R. Hogan Matthew Diller Wolbachia effect on egg mortality rate in mosquito population wolbachiaEffectOnEggMortalityRate 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. Wolbachia effect on adult mortality rate in mosquito population wolbachiaEffectOnAdultMortalityRate 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. 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 Wolbachia effect on larval mortality rate in mosquito population wolbachiaEffectOnLarvalMortalityRate William R. Hogan Matthew Diller 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. 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. Wolbachia effect on female fecundity in mosquito population wolbachiaEffectOnFecundity 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. 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. William R. Hogan Matthew Diller confidence interval William R. Hogan Matthew Diller 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. Wolbachia release interval wolbachiaReleaseInterval A seed release interval for a Wolbachia control measure. A seed release interval for a Wolbachia control measure. Matthew Diller William R. Hogan mean with confidence interval MeanWithConfidenceInterval Matthew Diller William R. Hogan A data structure that specifies both the sample mean and the confidence interval generated by the measurement process. mean with standard deviation MeanWithStandardDeviation William R. Hogan A data structure that specifies both the sample mean and the standard deviation generated by the measurement process. Matthew Diller number of Wolbachia-infected mosquitoes released per house wolbachiaSeedAdultsPerHouse 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 A vector control action specification that specifies the number of Wolbachia-infected adult mosquitoes to be released at each household. William R. Hogan clear Wolbachia upon vector migration clearWolbachiaOnMigration William R. Hogan Matthew Diller 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. 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. disease outcome with probability DiseaseOutcomeWithProbability William R. Hogan Matthew Diller A predicted data item expressing the probability that a disease outcome occurs during the disease course of an organism. A predicted data item expressing the probability that a disease outcome occurs during the disease course of an organism. date date A name of a temporal region that is systematized according to a particular calendar system, such as the Gregorian calendar. William R. Hogan Matthew Diller A name of a temporal region that is systematized according to a particular calendar system, such as the Gregorian calendar. ring diameter in meters ringDiameterInMeters 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. 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. Matthew Diller Wolbachia effect on mating probability wolbachiaEffectOnMatingProbability 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 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. William R. Hogan minimum value minimumValue William R. Hogan A data item that specifies the smallest numerical value in a data set of scalar measurement data items. A data item that specifies the smallest numerical value in a data set of scalar measurement data items. Matthew Diller maximum value maximumValue A data item that specifies the largest numerical value in a data set of scalar measurement data itmes. Matthew Diller A data item that specifies the largest numerical value in a data set of scalar measurement data itmes. William R. Hogan statistical confidence confidence William R. Hogan Matthew Diller A predicted data item that estimates how reliable some method of statistical inference will be at estimating the population parameter of interest. A predicted data item that estimates how reliable some method of statistical inference will be at estimating the population parameter of interest. closure period true Matthew Diller A one-dimensional temporal region occupied by a place closure control strategy. A one-dimensional temporal region occupied by a place closure control strategy. William R. Hogan lower bound lowerBound 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. 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 fraction of vector adults affected fractionOfVectorIndividualsAffected 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. 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. fraction reduction of eggs fractionReductionOfEggs Matthew Diller 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. 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. William R. Hogan fraction reduction of larvae fractionReductionOfLarvae 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). 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). Matthew Diller vector bite radius biteRadius Matthew Diller 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. 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. William R. Hogan time between vector bites timeBetweenBites William R. Hogan A duration that measures the temporal interval between some vector bite n and some vector bite n+1. A duration that measures the temporal interval between some vector bite n and some vector bite n+1. Matthew Diller migration speed migrationSpeed Matthew Diller 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. 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. William R. Hogan shade affinity shadeAffinity 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. 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. Matthew Diller movement speed speedOfMovement 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. mortality rate mortalityRate William R. Hogan A rate measurement datum that specifies the percentage of organisms within a population that have died over a given time interval. A rate measurement datum that specifies the percentage of organisms within a population that have died over a given time interval. Matthew Diller ratio of outdoor to indoor ovisites ratioOfOutdoorToIndoorOvisites 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. upper bound upperBound 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. 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 standard deviation standardDeviation 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 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. quarantine period quarantinePeriod Matthew Diller A temporal region occupied by some process wherein one or more potentially infectious contact organisms (i.e., contacted organisms) are under physical isolation from other organisms within a population. A temporal region occupied by some process wherein one or more potentially infectious contact organisms (i.e., contacted organisms) are under physical isolation from other organisms within a population. William R. Hogan mosquito mating probability matingProbability An information content entity that specifies 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 An information content entity that specifies 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. affinity for buildings buildingAffinity 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. 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 linear distance travelled between oviposits straightTravelAfterOviposit 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. William R. Hogan Matthew Diller 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. eggs per brood eggsPerBrood Matthew Diller An average value that specifies the number of eggs produced during one reproductive cycle for each individual female within a population. An average value that specifies the number of eggs produced during one reproductive cycle for each individual female within a population. William R. Hogan efficacy efficacy A disposition of an organism to (i) undergo some bodily benefit that (ii) is triggered by a planned process. William R. Hogan A disposition of an organism to (i) undergo some bodily benefit that (ii) is triggered by a planned process. Matthew Diller 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). prodromal period Matthew Diller 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. 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. fulminant period 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. 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. Matthew Diller vector bite probability biteProbability A predicted data item that specifies the frequency with which 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). A predicted data item that specifies the frequency with which 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 male mosquito mating radius maleMatingRadius 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. 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 infectious disease control strategy cover radius coverRadius 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. 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. species of treated organism speciesOfTreatedOrganism 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. An identifier curated by the NCBI taxonomy database that specifies the taxonomic classification of some organism that is the recipient of some treatment. Matthew Diller drug identifier drugId An identifier that denotes a drug product. Matthew Diller William R. Hogan An identifier that denotes a drug product. mean median minimum maximum summary statistics data structure MeanMedianMinimumMaximum A data structure that holds the mean, median, minimum value, and maximum value of one set of measurement data. A data structure that holds the mean, median, minimum value, and maximum value of one set of measurement data. William R. Hogan Matthew Diller heterogenous carrying capacity heterogenousCarryingCapacity William R. Hogan Matthew Diller 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. 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. seed site Class was originally created to correspond with an element from Apollo XSD v3.1.0. Matthew Diller 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. 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. William R. Hogan seed release interval William R. Hogan Matthew Diller A vector control action specification that is realized by releasing artificially-infected vector organisms at the specified time intervals. 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. vector release site action specification 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. Matthew Diller William R. Hogan A vector control action specification that specifies the location of vector release sites according to some predetermined spatial interval. number of artificially-infected vectors released per house William R. Hogan A vector control action specification that specifies the number of artificially-infected vectors to be released at each household. Matthew Diller 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. clear infection upon vector migration Class was originally created to correspond with an element from Apollo XSD v3.1.0. 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. 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. SNOMED concept identifier SnomedId An identifier curated by IHTSDO that refers to some representational unit within its class hierarchy. An identifier curated by IHTSDO that refers to some representational unit within its class hierarchy. Matthew Diller William R. Hogan probability Probability Matthew Diller 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'. 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. 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. minimum eggs per oviposition site minimumEggsPerOviposition 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. 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 age-dependent fecundity reduction ageDependentFecundityReduction 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). 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). carrying capacity per house carryingCapacityPerHouse An epidemic simulator action specification that specifies the maximum number of larvae that can exist across all ovisites in a given house. William R. Hogan Matthew Diller An epidemic simulator action specification that specifies the maximum number of larvae that can exist across all ovisites in a given house. Mosquitos can sense eggs in ovisite so tend to lay in places not at max. reactive control measure operator reactiveControlMeasureOperator William R. Hogan Matthew Diller 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. 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. gonotrophic period duration true Matthew Diller A time measurement datum of the length of the temporal interval occupied by a gonotropic period. A time measurement datum of the length of the temporal interval occupied by a gonotropic period. William R. Hogan description description William Hogan Matthew Diller A textual entity that specifies characteristics of some entity. A textual entity that specifies characteristics of some entity. parametric probability distribution ParametricProbabilityDistribution Matthew Diller 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). 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). William R. Hogan seed infections into vector population control measure 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. 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. Matthew Diller ovisite carrying capacity Matthew Diller A predicted data item that is the maximum value of larvae that some ovisite is capable of sustaining. William R. Hogan A predicted data item that is the maximum value of larvae that some ovisite is capable of sustaining. geographical migration of organism 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. 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. Matthew Diller cut-off point specification cutTailAt Matthew Diller 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. 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. prodromal period duration William R. Hogan A duration that measures a temporal region occupied by a prodromal period. Matthew Diller fulminant period duration William R. Hogan Matthew Diller A duration that measures a temporal region occupied by a fulminant period. identifier of species of diseased organism speciesWithDiseasae 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. 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. William R. Hogan Matthew Diller identifier for species of case speciesOfCase William R. Hogan Matthew Diller An identifier curated by the NCBI taxonomy database that has been used to identify the species of some organism that meets a case definition. An identifier curated by the NCBI taxonomy database that has been used to identify the species of some organism that meets a case definition. travel-related infectious disease control strategy An infectious disease control strategy that has an objective specification of preventing infection acquisition by organisms 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 infectious disease control strategy to prevent infection acquisition by individuals traveling from one ecosystem to another ecosystem travel recommendation 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 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 William R. Hogan travel recommendation infectious disease control strategy contact isolation control measure ContactIsolationControlMeasure 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. 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 colonization duration colonizationDuration A duration that measures the temporal interval occupied by some colonization. Matthew Diller A duration that measures the temporal interval occupied by some colonization. William R. Hogan identifier of species of population populationSpecies William R. Hogan A taxonomy identifier curated by the National Center for Biotechnology Information that specifies the taxonomic classification of some population of organisms. An identifier curated by the National Center for Biotechnology Information that specifies the taxonomic classification of some population of organisms. Matthew Diller RxNorm drug concept identifier RxNormId 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. LOINC identifier LoincId 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. An identifier curated by the Regenstrief Institute to be used as a standard way of denoting each term in the LOINC database. Matthew Diller laboratory test LOINC identifier testLoincId Matthew Diller A LOINC identifier that refers to some clinical laboratory test conducted in a particular context.. A LOINC identifier that refers to some clinical laboratory test conducted in a particular context.. Willliam R. Hogan PubMed identifier pubMedId 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. 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 ORCID orcId An identifier curated by ORCID, Inc. to denote some academic author. William R. Hogan Matthew Diller An identifier curated by ORCID, Inc. to denote some academic author. count of disease cases CaseCount Matthew Diller William R. Hogan A count of individuals in a population who meet the criteria of some case definition during some time interval. A count of individuals in a population who meet the criteria of some case definition during some time interval. count of cases in an epidemic EpidemicCaseCounts A count of disease cases in an infected population that meet the case definition criteria within a particular epidemic interval. William R. Hogan Matthew Diller A count of disease cases in an infected population that meet the case definition criteria within a particular epidemic interval. insecticide-treated net control measure InsecticideTreatedNetControlMeasure Matthew Diller 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. 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. William R. Hogan schedule Schedule 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. 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 population colonization census PopulationColonizationCensus A population census about the organisms specific to that population that were the host in some colonization acquisition. Matthew Diller A population census about the organisms specific to that population that were the host in some colonization acquisition. William R. Hogan drug treatment efficacy drugTreatmentEfficacy Matthew Diller The efficacy measured for some instance(s) of drug treatment for preventing or ameliorating some disease outcome. The efficacy measured for some instance(s) of drug treatment for preventing or ameliorating some disease outcome. 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. William R. Hogan latitude and longitude coordinate pair LatLongPair 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. William R. Hogan Matthew Diller 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. age in years datum ageInYears Matthew Diller 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. 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. William R. Hogan contamination period duration contaminationDuration William R. Hogan A duration that measures a temporal region occupied by some contamination. A duration that measures a temporal region occupied by some contamination. Matthew Diller healthcare facility identifier healthcareFacilityId Matthew Diller A healthcare facility identifier that refers to some architectural structure that is the bearer of some healthcare function. A healthcare facility identifier that refers to some architectural structure that is the bearer of some healthcare function. William R. Hogan disease transmission model identifier modelId William R. Hogan An identifier that refers to some disease transmission model model. An identifier that refers to some disease transmission model model. Matthew Diller facility identifier FacilityId An identifier that denotes some architectural structure. Matthew Diller An identifier that denotes some architectural structure. William R. Hogan taxonomy identifier taxonId William R. Hogan An identifier that denotes a biological taxonomic group. Matthew Diller disease case identifier caseId 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. infection acquisition through sexual activity with infectious host 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. rate of hydrological precipitation 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 mean 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. William R. Hogan Matthew Diller mean air temperature Matthew Diller William R. Hogan An average value that takes, as input, some set of air temperature measurement data that were recorded over a particular duration of time. potentially infectious sexual contacting Matthew Diller William R. Hogan 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. 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 host population population of host organisms prioritization scheme for control measure controlMeasureNamedPrioritizationScheme Matthew Diller An action specification that is part of an infectious disease control strategy that has at least one rule pertaining to some control measure. An action specification that is part of an infectious disease control strategy that has at least one rule pertaining to some control measure. William R. Hogan one-way sensitivity analysis of a continuous variable William R. Hogan Matthew Diller 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. 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. citation identifier referenceId Matthew Diller An identifier that is an integer numeral that denotes some citation. An identifier that is an integer numeral that denotes some citation. William R. Hogan location of sampling process whereSampled William R. Hogan A geographic region that contains a sampling process. A geographic region that contains a sampling process. Matthew Diller infection acquisition from vertical transmission Matthew Diller 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. 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. William R. Hogan congenital infection acquisition infection acquisition from mother-to-child transmission source code 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. Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based William R. Hogan software source code version control repository compiling software A planned process that converts human-written or curated software source code into a machine-executable or interpretable set of instructions. 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. William R. Hogan process of compiling software compiled software code A software that is the specified output of some compilation of software process William R. Hogan machine instructions compiled from software source code scale-free network model An algorithm that models some scale-free network. Matthew Diller William R. Hogan scale-free network William R. Hogan 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 synthetic ecosystem data set SyntheticEcosystem Matthew Diller 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. The interactions between each organism as they move between these facilities may also be included in the data set. William R. Hogan conditional probability conditionalProbability William R. Hogan A probability whose value is dependent upon the occurrence, known or presumed, of some process. Matthew Diller A probability whose value is dependent upon the occurrence, known or presumed, of some process. probability of infection over time probabilityOfInfectionOverTime Matthew Diller A conditional probability whose value is dependent upon the duration of some colonization or infection. William R. Hogan A conditional probability whose value is dependent upon the duration of some colonization or infection. epidemic threshold William R. Hogan A data item that specifies the number of susceptible organisms necessary for an epidemic to occur within a population. Matthew Diller human travel Matthew Diller A geographical migration of an organism belonging to the species Homo sapiens. William R. Hogan human air travel William R. Hogan Matthew Diller 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. human mobility data item 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 software license A copyright license that is about some software and contains one or more conditional specifications that specify the use and redistribution of the software. A copyright license that is about some software and contains one or more conditional specifications that specify the use and redistribution of the software. William R. Hogan Matthew Diller complete software license identifier SoftwareLicenseIdentification William R. Hogan Matthew Diller An identifier that refers to a specific software license. An identifier that refers to a specific software license. software license version identifier licenseVersion Matthew Diller An identifier that, as part of a complete software license identifier, refers to one specific version of the software license. An identifier that, as part of a complete software license identifier, refers to one specific version of the software license. William R. Hogan software license identifier licenseName William R. Hogan Matthew Diller An identifier that refers to all versions of a specific software license. An identifier that refers to all versions of a specific software license. software license URL licenseLocation Matthew Diller A unique resource locator that constitutes a reference to some software license. William R. Hogan A unique resource locator that constitutes a reference to some software license. population dynamics model William R. Hogan Matthew Diller An algorithm that simulates changes in the size and life stage distribution of a population or populations of organisms of a particular biological taxon. An algorithm that simulates changes in the size and life stage distribution of a population or populations of organisms of a particular biological taxon. model of population dynamics disease surveillance objective specification Matthew Diller 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. 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. William R. Hogan disease surveillance objective specification mortality data William R. Hogan Matthew Diller 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. 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. population mortality data set pathogen evolution model Matthew Diller Simulation software that simulates the evolution over time of a particular pathogen of a particular biological taxon. Simulation software that simulates the evolution over time of a particular pathogen of a particular biological taxon. William R. Hogan pathogen evolution model software disease surveillance A planned process that is the realization of a disease surveillance objective specification. Matthew Diller A planned process that is the realization of a disease surveillance objective specification. William R. Hogan self-initiated travel avoidance behavior 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. 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. William R. Hogan Matthew Diller social interaction data item William R. Hogan Matthew Diller 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). 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). Susceptible-Infected-Susceptible model Matthew Diller 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. 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. William R. Hogan Susceptible-Infected-Resistant 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. William R. Hogan Matthew Diller 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. contact tracing Matthew Diller An infectious disease control strategy that identifies and treats contacted organisms in a host population. An infectious disease control strategy that identifies and treats contacted organisms in a host population. William R. Hogan Susceptible-Exposed-Infectious-Recovered model William R. Hogan Matthew Diller 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. 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. metapopulation disease transmission 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. 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. William R. Hogan Matthew Diller two-strain Susceptible-Infectious-Resistant 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. disease surveillance data A data set that is about some disease surveillance. A data set that is about some disease surveillance. Matthew Diller William R. Hogan disease transmission tree estimator An algorithm that has specified output some transmission tree. Matthew Diller William R. Hogan An algorithm that has specified output some transmission tree. mechanical flight function Matthew Diller A function inhering in some device that is realized by some movement process in the atmosphere in which the device is participant in. A function inhering in some device that is realized by some movement process in the atmosphere in which the device is participant in. William R. Hogan disease forecasting software Matthew Diller Simulation software 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 by some time in the future relative to when the data items are created. William R. Hogan disease forecasting disease transmission forecasting software that forecasts disease transmission case series CaseSeries An investigation that has, as part, a population survey with an objective to count all participants in some disease outcome or some exposure process. An investigation that has, as part, a population survey with an objective to count all participants in some disease outcome or some exposure process. Matthew Diller William R. Hogan case series data set A data set that is the output of a case series investigation. A data set that is the output of a case series investigation. Matthew Diller William R. Hogan epidemic data set A data set about an instance of an epidemic. A data set about an instance of an epidemic. Matthew Diller William R. Hogan disease transmission model software Matthew Diller William R. Hogan data format converter Matthew Diller William R. Hogan phylogenetic tree constructor software data visualizer software Matthew Diller William R. Hogan computational modeling toolkit Matthew Diller William R. Hogan data parsing 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 parsing process data reading process reading data synthetic ecosystem constructor A software that when compiled and run, has specified output of an agent-level ecosystem data set. William R. Hogan example: Synthia, SPEW software for creating a synthetic ecosystem dataset synthetic ecosystem constructor software total fatal disease cases totalFatalCaseCount 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. 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. total disease cases totalCaseCount William R. Hogan A data item that is the output of some infection case count. A data item that is the output of some infection case count. Matthew Diller employment status data item employmentStatus 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 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. William R. Hogan 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. contaminated abiotic thing contaminatedAbioticThing William R. Hogan Matthew Diller An abiotic ecosystem element that is participant in some biological contamination process. An abiotic ecosystem element that is participant in some biological contamination process. 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 dataset creating A planned process that has a data set as its specified output. William R. Hogan creating a data set data set creation dataset 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 A planned process that has a copyright license as its specified output. William R. Hogan copyright license creation creating a copyright license copyright license 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. Can be for any creative work including fiction. But the license itself is an ICE, and refers to real claims and obligations. William R. Hogan copyright license for a creative work data service software A software that implements a data service. William R. Hogan data service software TODO object_aggregate 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 Interval history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. antiviral drug The usage or intended usage of a drug product to act against a viral infection of a host. drug product http://purl.obolibrary.org/obo/dron.owl William Hogan William Hogan 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 environmental material A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. 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. http://purl.obolibrary.org/obo/envo.owl portion of environmental material water vapour 2013-10-10T07:58:18Z ENVO ENVO:01000266 ORCID:0000-0002-4366-3088 Perhaps a better relation between water vapour and water can be found in or added to RO? Water vapour is a vapour which is the gas phase of water. aqueous vapor aqueous vapour http://purl.obolibrary.org/obo/envo.owl water vapor atmospheric water vapour 2013-10-10T08:22:07Z Atmospheric water vapour is water vapour that is part of an atmosphere. ENVO ENVO:01000268 ORCID:0000-0002-4366-3088 atmospheric water vapor http://purl.obolibrary.org/obo/envo.owl hydrological precipitation process http://purl.obolibrary.org/obo/envo.owl precipitation Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity. "process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet) air temperature http://purl.obolibrary.org/obo/envo.owl Draft class. In discussion in Issue #278. A temperature that inheres in some portion of air. gaseous environmental material http://purl.obolibrary.org/obo/envo.owl This class is to be populated by inference. gas A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely. environmental system process 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. temperature of environmental material http://purl.obolibrary.org/obo/envo.owl The temperature of a environmental material. environmental material temperature temperature of air http://purl.obolibrary.org/obo/envo.owl air temperature The temperature of a air. website 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. FBcv:0000667 http://purl.obolibrary.org/obo/fbcv.owl pub_type journal 2012-07-10T04:08:06Z A publication issued on a regular, ongoing basis containing separate research articles and other writings such as reviews, comments and conference reports. FBcv:0000787 MeSH:D020492 Periodicals djs93 http://purl.obolibrary.org/obo/fbcv.owl pub_type definition is circular. Location William R. Hogan A site designated by some relative spatial orientation. An arbitrary part of the Earth defined by human-made boundaries and/or natural features such as rivers. Matthew Diller reproduction Reproduction http://purl.org/obo/owl/gene_ontology biological_process GO:0019952 GO:0050876 The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism. The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism. response to stress 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). 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. biological_process http://purl.obolibrary.org/obo/go.owl response to abiotic stress response to biotic stress defense response GO:0002217 GO:0006952 GO:0042829 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. antimicrobial peptide activity biological_process defence response defense/immunity protein activity http://purl.obolibrary.org/obo/go.owl physiological defense response inflammatory response GO:0006954 Inflammation 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. This term was improved by GO_REF:0000022. It was moved. Wikipedia:Inflammation biological_process http://purl.obolibrary.org/obo/go.owl eclose eclosion http://purl.org/obo/owl/gene_ontology biological_process The emergence of an adult insect from a pupa case. female pregnancy GO:0007565 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. Wikipedia:Gestation biological_process carrying of young gestation http://purl.obolibrary.org/obo/go.owl parturition GO:0007567 The reproductive process in which the parent is separated from its offspring either by giving birth to live young or by laying eggs. biological_process egg laying giving birth http://purl.obolibrary.org/obo/go.owl aging http://purl.org/obo/owl/gene_ontology GO:0016280 biological_process behavior Behavior 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. The internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. Wikipedia:Behavior behavioral response to stimulus behaviour behavioural response to stimulus biological_process http://purl.obolibrary.org/obo/go.owl mating behavior GO:0007617 The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes. Wikipedia:Mating_behaviour biological_process http://purl.obolibrary.org/obo/go.owl mating behaviour biological process http://purl.obolibrary.org/obo/ido.owl 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. biological_process multicellular organismal aging 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). GO:0010259 biological_process http://purl.obolibrary.org/obo/go.owl regulation of cell death 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. GO:0010941 biological_process http://purl.obolibrary.org/obo/go.owl oviposition http://purl.org/obo/owl/gene_ontology biological_process modulation by virus of host morphology or physiology GO:0019048 GO:0044792 Reactome:REACT_6323 The process in which a virus effects a change in the structure or processes of its host organism. VZ:886 biological_process host-virus interaction http://purl.obolibrary.org/obo/go.owl 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 interaction virus-host process induction by virus of host apoptotic process GO:0019051 The set of viral processes that induce an apoptotic process in infected host cells, facilitating release and spread of progeny virions. activation by virus of host apoptosis activation by virus of host apoptotic programmed cell death activation of apoptosis in host by virus biological_process http://purl.obolibrary.org/obo/go.owl induction by virus of host apoptosis induction by virus of host apoptotic programmed cell death induction of apoptosis in host by virus modulation by virus of host process GO:0019054 Reactome:REACT_6222 The process in which a virus effects a change in the processes and activities of its host organism. biological_process http://purl.obolibrary.org/obo/go.owl modification by virus of host cellular process modulation of cellular process in host by virus 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 reproductive behavior http://purl.org/obo/owl/gene_ontology biological_process reproductive process A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GO:0022414 biological_process http://purl.obolibrary.org/obo/go.owl developmental process http://purl.org/obo/owl/gene_ontology biological_process multicellular organism reproduction GO:0032504 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. biological_process http://purl.obolibrary.org/obo/go.owl multicellular organismal reproductive behavior http://purl.org/obo/owl/gene_ontology biological_process social 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. Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. GO:0035176 Wikipedia:Social_behavior biological_process cooperative behavior http://purl.obolibrary.org/obo/go.owl social behaviour modification of morphology or physiology of other organism 2011-04-21T01:31:51Z GO:0035821 The process in which an organism effects a change in the structure or processes of a second organism. biological_process http://purl.obolibrary.org/obo/go.owl regulation of morphology of other organism regulation of morphology or physiology of other organism regulation of physiological process of other organism regulation of physiology of other organism rfoulger induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process 2012-10-09T15:44:29Z 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. GO:0039651 activation of host caspases by virus biological_process http://purl.obolibrary.org/obo/go.owl induction by virus of host caspase activity rfoulger regulation of programmed cell death Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GO:0043067 GO:0043070 biological_process http://purl.obolibrary.org/obo/go.owl regulation of non-apoptotic programmed cell death modification by symbiont of host morphology or physiology GO:0044003 The process in which a symbiont organism effects a change in the structure or processes of its host organism. biological_process http://purl.obolibrary.org/obo/go.owl symbiosis, encompassing mutualism through parasitism An interaction between two organisms living together in more or less intimate association. The term host is usually used for the larger (macro) of the two members of a symbiosis. The smaller (micro) member is called the symbiont organism. Microscopic symbionts are often referred to as endosymbionts. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Note that this term encompasses all symbiotic relationships between species along a continuum from mutualism through to parasitism, as outlined in the definition. entry into host 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. interspecies interaction between organisms Any process in which an organism has an effect on an organism of a different species. modulation of programmed cell death in other organism 2012-03-20T04:48:41Z A process in which an organism modulates the frequency, rate or extent of programmed cell death in a second organism. GO:0044531 biological_process http://purl.obolibrary.org/obo/go.owl janelomax multi-organism reproductive process 2012-09-19T15:56:30Z A biological process that directly contributes to the process of producing new individuals, involving another organism. GO:0044703 biological_process http://purl.obolibrary.org/obo/go.owl janelomax multi-organism reproductive behavior 2012-09-19T16:02:12Z GO:0044705 The specific behavior of an organism that is associated with reproduction involving another organism of the same or different species. biological_process http://purl.obolibrary.org/obo/go.owl janelomax multicellular organismal reproductive process GO:0048609 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. biological_process http://purl.obolibrary.org/obo/go.owl organismal reproductive process reproductive process in a multicellular organism regulation of biological 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. GO:0050789 GO:0050791 biological_process http://purl.obolibrary.org/obo/go.owl regulation of physiological process regulation of cellular 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. GO:0050794 GO:0051244 biological_process http://purl.obolibrary.org/obo/go.owl regulation of cellular physiological process response to stimulus 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. GO:0050896 GO:0051869 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. biological_process http://purl.obolibrary.org/obo/go.owl physiological response to stimulus establishment of localization establishment of localization http://purl.obolibrary.org/obo/ido.owl The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location. establishment of localization interaction with host An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism. GO:0051701 biological_process http://purl.obolibrary.org/obo/go.owl multi-organism process A biological process which involves another organism of the same or different species. modification of morphology or physiology of other organism involved in symbiotic interaction GO:0051817 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. biological_process http://purl.obolibrary.org/obo/go.owl 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 of other organism during symbiotic interaction regulation of morphology or physiology 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 modulation by symbiont of host programmed cell death 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. GO:0052040 GO:0052152 biological_process http://purl.obolibrary.org/obo/go.owl modulation by symbiont of host non-apoptotic programmed cell death modulation of host PCD 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 organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. GO:0012504 GO:0052042 GO:0052044 GO:0052045 GO:0052153 GO:0052397 GO:0052400 activation by organism of host programmed cell death activation by organism of non-apoptotic programmed cell death in other organism activation by organism of programmed cell death in other organism during symbiotic interaction activation by symbiont of host programmed cell death biological_process enhancement of host programmed cell death enhancement of host programmed cell death by organism http://purl.obolibrary.org/obo/go.owl induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction induction by organism of programmed cell death in other organism during symbiotic interaction induction by organism of programmed cell death in other organism involved in symbiotic interaction induction by symbiont of host programmed cell death induction of non-apoptotic programmed cell death by other organism positive regulation by symbiont of host non-apoptotic programmed cell death stimulation by symbiont of host programmed cell death upregulation by symbiont of host programmed cell death positive regulation by symbiont of host apoptotic process 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. GO:0033669 GO:0052030 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'. activation by organism of host apoptosis activation by organism of host apoptotic programmed cell death activation by symbiont of host apoptosis biological_process http://purl.obolibrary.org/obo/go.owl 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 positive regulation by symbiont of host apoptosis stimulation by symbiont of host apoptosis 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 modulation of programmed cell death in other organism involved in symbiotic interaction 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. GO:0052248 GO:0052459 biological_process http://purl.obolibrary.org/obo/go.owl modulation by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction modulation of programmed cell death in other organism during symbiotic interaction positive regulation by organism of apoptotic process 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. GO:0052388 GO:0052501 activation by organism of apoptosis in other organism during symbiotic interaction activation by organism of apoptotic programmed cell death in other organism during symbiotic interaction biological_process http://purl.obolibrary.org/obo/go.owl induction by organism of apoptosis in other organism during symbiotic interaction induction by organism of apoptosis in other organism involved in 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 apoptosis in other organism involved in symbiotic interaction positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction positive regulation by organism of apoptotic programmed cell death in other organism during symbiotic interaction stimulation by organism of apoptosis 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 positive regulation of apoptotic process by virus Any viral process that activates or increases the frequency, rate or extent of cell death by apoptotic process. GO:0060139 biological_process http://purl.obolibrary.org/obo/go.owl positive regulation of apoptosis by virus modulation by virus of host cell cycle Any viral process that modulates the rate or extent of progression through the cell cycle. GO:0060153 VZ:1636 biological_process http://purl.obolibrary.org/obo/go.owl 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 post-mating oviposition http://purl.org/obo/owl/gene_ontology biological_process biological regulation Any process that modulates a measurable attribute of any biological process, quality or function. GO:0065007 biological_process http://purl.obolibrary.org/obo/go.owl regulation regulation of biological quality 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. GO:0065008 biological_process http://purl.obolibrary.org/obo/go.owl regulation of biological attribute regulation of biological characteristic organism emergence from protective structure http://purl.org/obo/owl/gene_ontology biological_process measurement unit label unitId 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. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. Examples of measurement unit labels are liters, inches, weight per volume. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label objective specification 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? OBI Plan and Planned Process/Roles Branch OBI_0000217 PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel 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. objective specification purpose of a study; support of hypothesis, discovery of new information action specification Alan Ruttenberg OBI Plan and Planned Process branch Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take label 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 GROUP: IAO http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n label software GROUP: OBI PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot 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 software data item 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. PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data item 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. Data items include counts of things, analyte concentrations, and statistical summaries. 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 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. data symbol 20091104, MC: this needs work and will most probably change PERSON: Jonathan Rees a smallish, word-like datum... symbol information content entity OBI_0000142 PERSON: Chris Stoeckert 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 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. scalar measurement datum 1 1 10 feet. 3 ml. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form PERSON: Alan Ruttenberg PERSON: Melanie Courtot 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. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. directive information entity 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 An information content entity whose concretizations indicate to their bearer how to realize them in a process. PERSON: Alan Ruttenberg PERSON: Bjoern Peters 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 algorithm 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. OBI_0000270 PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. Philippe Rocca-Serra PlanAndPlannedProcess Branch adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm data set OBI_0000042 dataSets 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 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. Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). data set group:OBI person:Allyson Lister person:Chris Stoeckert plan specification 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 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. Alan Ruttenberg Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved OBI Plan and Planned Process branch OBI_0000344 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. plan specification measurement datum 2/2/2009 is_specified_output of some assay? A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 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,}. OBI_0000305 group:OBI measurement datum person:Chris Stoeckert 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. GROUP: IAO 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 version number time measurement datum 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A scalar measurement datum that is the result of measuring a temporal interval Person:Alan Ruttenberg time stamped measurement datum time sampled measurement data set 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 pmid:20604925 - time-lapse live cell microscopy name sexual activity http://purl.obolibrary.org/obo/MF.owl behavior_ontology George Gkoutos "Behaviour related to the activity which primary purpose is the sexual reproduction." [NBO:GVG] 2011-04-14T01:03:39Z Mus musculus House mouse Mus musculus William R. Hogan Virus Poxviridae Chordopoxvirinae Orthopoxvirus Monkeypox virus Mirela L Vasconcelos monkey pox virus Variola virus H5N1 subtype H5N1 subtype of Influenza A virus Herpesviridae GC_ID:1 ncbi_taxonomy Alphaherpesvirinae GC_ID:1 ncbi_taxonomy Varicellovirus GC_ID:1 ncbi_taxonomy Human herpesvirus 3 GC_ID:1 HHV-3 Human alphaherpesvirus 3 Human herpes virus 3 VZV Varicella Zoster Virus Varicella-zoster virus ncbi_taxonomy varicella zoster virus VZV varicella-zoster virus VZV Human herpes virus 3 varicella zoster virus VZV Varicella-zoster virus VZV Human alphaherpesvirus 3 HHV-3 varicella-zoster virus VZV Varicella Zoster Virus Suid herpesvirus 1 Alphaherpesvirus pseudorabies virus PRV Aujeszky's disease virus GC_ID:1 NCBITaxon:44156 PRV Pseudorabies Virus PRV Pseudorabies virus Suid herpesvirus type 1 ncbi_taxonomy Suid herpesvirus type 1 Alphaherpesvirus pseudorabies virus PRV Pseudorabies Virus PRV PRV Pseudorabies virus Aujeszky's disease virus Hepadnaviridae GC_ID:1 hepatitis B-type viruses ncbi_taxonomy hepatitis B-type viruses Orthohepadnavirus GC_ID:1 mammalian hepatitis B-type viruses ncbi_taxonomy mammalian hepatitis B-type viruses Hepatitis B virus GC_ID:1 HBV Human hepatitis B virus hepatitis B virus (HBV) hepatitis B virus HBV hepatitis B virus, HBV human hepatitis B virus HBV ncbi_taxonomy Human hepatitis B virus HBV hepatitis B virus HBV hepatitis B virus, HBV hepatitis B virus (HBV) human hepatitis B virus HBV Escherichia coli O157 GC_ID:11 ncbi_taxonomy Aedini canis group GC_ID:11 ncbi_taxonomy phagocytophilum group GC_ID:11 ncbi_taxonomy phagocytophila group phagocytophila group Reoviridae Mirela L Vasconcelos Rotavirus Mirela L Vasconcelos Rotaviruses Togaviridae Alphavirus Alphavirus Alphaviridae GC_ID:1 arboviruses group A ncbi_taxonomy Alphaviridae arboviruses group A Eastern equine encephalitis virus Eastern equine encephalomyelitis virus GC_ID:1 eastern equine encephalomyelitis EEE eastern equine encephalomyelitis virus EEEV ncbi_taxonomy eastern equine encephalomyelitis virus EEEV eastern equine encephalomyelitis EEE Eastern equine encephalomyelitis virus Western equine encephalitis virus GC_ID:1 Western equine encephaliomyelitis virus Western equine encephalomyelitis virus ncbi_taxonomy Western equine encephalomyelitis virus Western equine encephaliomyelitis virus Rubivirus GC_ID:1 ncbi_taxonomy Rubella virus GC_ID:1 ncbi_taxonomy Flaviviridae Flavivirus Flavivirus GC_ID:1 arboviruses group B ncbi_taxonomy arboviruses group B Dengue virus group Dengue virus 1 Dengue virus 2 Dengue virus 3 Dengue virus 4 Japanese encephalitis virus group GC_ID:1 Japanese encephalitis viruses ncbi_taxonomy Japanese encephalitis viruses West Nile virus GC_ID:1 WNV ncbi_taxonomy WNV Yellow fever virus Flavivirus febricis GC_ID:1 YFV ncbi_taxonomy yellow fever virus YFV Flavivirus febricis YFV yellow fever virus YFV Hepacivirus Hepatitis C virus group Hepatitis C viruses Hepatitis C-like viruses Mirela L Vasconcelos Hepatitis C virus Mirela L Vasconcelos hepatitis C virus HCV human hepatitis C virus human hepatitis C virus HCV human hepatitis virus C HCV post-transfusion hepatitis non A non B virus Coronaviridae http://purl.obolibrary.org/obo/obi.owl Coronaviridae Chlamydia/Chlamydophila group Mirela L Vasconcelos Mononegavirales Paramyxoviridae Paramyxovirinae Mumps virus GC_ID:1 ncbi_taxonomy Morbillivirus Mirela L Vasconcelos Morbilliviruses Measles virus Pneumoviridae Mirela L Vasconcelos Pneumovirinae Pneumovirus Mirela L Vasconcelos Filoviridae Rhabdoviridae Mirela L Vasconcelos Lyssavirus Mirela L Vasconcelos Rabies lyssavirus Mirela L Vasconcelos Rabies virus Orthomyxoviridae Influenza A virus spotted fever group GC_ID:11 PMID:9734038 ncbi_taxonomy typhus group GC_ID:11 ncbi_taxonomy H1N1 subtype H1N1 subtype of Influenza A virus H2N2 subtype H2N2 subtype of Influenza A virus Influenza B virus Influenza virus type B Mirela L Vasconcelos Bunyaviridae Bunyaviridae GC_ID:1 ncbi_taxonomy Mirela L Vasconcelos Phlebovirus Mirela L Vasconcelos Phleboviruses Rift Valley fever virus Mirela L Vasconcelos Hantavirus GC_ID:1 Hantaviurs ncbi_taxonomy Hantaviurs Retroviridae Lentivirus Lentivirinae Primate lentivirus group Primate immunodeficiency viruses Human immunodeficiency virus 1 HIV-1 Human immunodeficiency virus type 1 human immunodeficiency virus 1 HIV-1 human immunodeficiency virus HIV-1 human immunodeficiency virus type 1 HIV 1 human immunodeficiency virus type 1 HIV-1 human immunodeficiency virus type 1 HIV1 human immunodeficiency virus type 1, HIV-1 human immunodeficiency virus type I HIV-1 human immunodeficiency virus type-1 HIV-1 human immunodeficiency virus-1 HIV-1 Human immunodeficiency virus 2 HIV type 2 HIV-2 Human immunodeficiency virus type 2 Human immunodeficiency virus-2 human immunodeficiency virus type 2 HIV-2 human immunodeficiency virus type 2, HIV-2 Teleostomi Euteleostomi bony vertebrates Brucellaceae Brucellaceae Breed et al. 1957 GC_ID:11 ncbi_taxonomy Brucellaceae Breed et al. 1957 Legionellales GC_ID:11 Legionellaceae group Legionellales Garrity et al. 2005 PMID:16280474 ncbi_taxonomy Legionellales Garrity et al. 2005 Legionellaceae group Enoplea GC_ID:1 ncbi_taxonomy H3N2 subtype H3N2 subtype of Influenza A virus H7N2 subtype H7N2 subtype of Influenza A virus H7N7 subtype H7N7 subtype of Influenza A virus H5N2 subtype H5N2 subtype of Influenza A virus Caliciviridae Mirela L Vasconcelos Picornaviridae Enterovirus Ecdysozoa Human poliovirus 1 Human poliovirus type 1 Poliovirus type 1 poliovirus type 1 PV1 Human poliovirus 3 Human poliovirus type 3 Poliovirus type 3 Hepatovirus Mirela L Vasconcelos Hepatovirus A Hepatitis A virus Mirela L Vasconcelos Aphthovirus Mirela L Vasconcelos Foot-and-mouth disease virus Foot and mouth disease virus Mirela L Vasconcelos foot and mouth disease virus FMDV foot-and-mouth disease virus FMDV Proteobacteria Alphaproteobacteraeota Mirela L Vasconcelos purple bacteria purple bacteria and relatives purple non-sulfur bacteria purple photosynthetic bacteria purple photosynthetic bacteria and relatives Gammaproteobacteria Mirela L Vasconcelos Proteobacteria gamma subdivision Purple bacteria, gamma subdivision gamma proteobacteria gamma subdivision gamma subgroup Firmicutes Gram-postive bacterium Hepatitis delta virus Hepatitis D virus Mirela L Vasconcelos hepatitis delta virus HDV Dengue virus Staphylococcus Aurococcus Staphylococcus Vibrio cholerae O1 Mirela L Vasconcelos Vibrio cholerae serogroup O1 Staphylococcus aureus Micrococcus aureus Micrococcus pyogenes Staphlococcus pyogenes citreus Staphylococcus aureus Staphylococcus pyogenes aureus Streptococcus aureus Conoidasida GC_ID:1 ncbi_taxonomy Respiratory syncytial virus Mirela L Vasconcelos respiratory syncytial virus RS respiratory syncytial virus RS virus respiratory syncytial virus RSV Streptococcaceae Mirela L Vasconcelos Streptococcus Mirela L Vasconcelos Streptococcus pneumoniae Diplococcus pneumoniae Micrococcus pneumoniae Mirela L Vasconcelos Archelosauria Archosauria-Testudines GC_ID:1 PMID:22839753 PMID:25450099 Testudines + Archosauria group ncbi_taxonomy Archosauria-Testudines Testudines + Archosauria group Middle East respiratory syndrome coronavirus Dipnotetrapodomorpha Vibrionales Mirela L Vasconcelos Vibrionaceae group Pasteurellales Mirela L Vasconcelos Pasteruellaceae group Spirochaetales GC_ID:11 PMID:11075904 PMID:11542017 PMID:16558735 PMID:1917844 PMID:23908650 ncbi_taxonomy spirochetes spirochetes Spirochaetaceae GC_ID:11 PMID:23908650 Treponemataceae ncbi_taxonomy Treponemataceae Borrelia GC_ID:11 PMID:24744012 PMID:8863409 PMID:8863416 Relapsing Fever Borrelia ncbi_taxonomy Relapsing Fever Borrelia Bacillales Bacillus Enterovirus A Coxsackievirus A Enterovirus EV-A Human coxsackievirus A Human enterovirus A Mirela L Vasconcelos Enterovirus C Enterovirus EV-C Human enterovirus C Poliovirus Enterovirus D Bacillus anthracis Bacillus cereus var. anthracis Bacteridium anthracis Mirela L Vasconcelos anthrax anthrax bacterium Norovirus Mirela L Vasconcelos Norwalk-like viruses Boreoeutheria Boreoeutheria Boreotheria GC_ID:1 PMID:11743200 PMID:11791233 ncbi_taxonomy Boreotheria Trichinella murrelli GC_ID:1 NCBITaxon:92178 PMID:10701576 Trichinella T5 Trichinella sp. T5 ncbi_taxonomy Trichinella sp. T5 Trichinella T5 Dorylaimia GC_ID:1 ncbi_taxonomy Saccharomycotina GC_ID:1 ncbi_taxonomy true yeasts true yeasts Pezizomycotina Euascomycota GC_ID:1 ncbi_taxonomy Euascomycota Eurotiomycetes GC_ID:1 Loculoascomycetes NCBITaxon:147540 Plectomycetes bitunicate ascomycetes ncbi_taxonomy Plectomycetes bitunicate ascomycetes Loculoascomycetes Rhinovirus A Clostridium Anaerobacter GC_ID:11 NCBITaxon:69207 PMID:26643615 ncbi_taxonomy Anaerobacter Clostridioides difficile Bacillus difficilis Clostridium difficile Mirela L Vasconcelos Peptoclostridium difficile Clostridium tetani Bacillus tetani GC_ID:11 ncbi_taxonomy Bacillus tetani Clavispora/Candida clade GC_ID:1 ncbi_taxonomy Galloanserae GC_ID:1 Galloanseri ducks, geese, chickens, fowl, quail, currasows and allies ncbi_taxonomy ducks, geese, chickens, fowl, quail, currasows and allies Galloanseri Treponema GC_ID:11 Microspironema PMID:23961314 PMID:9019153 PMID:9734025 ncbi_taxonomy Microspironema Onygenales incertae sedis GC_ID:1 NCBITaxon:34383 ncbi_taxonomy Treponema pallidum GC_ID:11 Microspironema pallidum Spirillum pallidum Spirochaeta pallida Spironema pallidum ncbi_taxonomy Microspironema pallidum Spironema pallidum Spirillum pallidum Spirochaeta pallida Treponema pallidum subsp. pallidum GC_ID:11 Treponema pallidum pallidum ncbi_taxonomy syphilis treponeme syphilis treponeme Treponema pallidum pallidum Listeria GC_ID:11 Listerella PMID:10408878 PMID:15709360 PMID:1713054 PMID:1899799 PMID:8427807 PMID:8782674 PMID:9226919 PMID:9542083 ncbi_taxonomy Listerella Listeria ivanovii GC_ID:11 Listeria bulgarica Listeria monocytogenes subsp. perhaemolytica Listeria perhaemolytica PMID:8782698 ncbi_taxonomy Listeria bulgarica Listeria monocytogenes subsp. perhaemolytica Listeria perhaemolytica Listeria monocytogenes Bacterium monocytogenes Bacterium monocytogenes hominis Corynebacterium infantisepticum Corynebacterium parvulum Erysipelothrix monocytogenes GC_ID:11 Listerella hepatolytica Listeria momocytogenes Lysteria monocytogenes NCBITaxon:1634566 PMID:17773427 PMID:1906732 PMID:8782698 ncbi_taxonomy Listerella hepatolytica Erysipelothrix monocytogenes Bacterium monocytogenes hominis Bacterium monocytogenes Corynebacterium parvulum Listeria momocytogenes Lysteria monocytogenes Corynebacterium infantisepticum Plasmodiidae Mirela L Vasconcelos Listeria grayi GC_ID:11 Listeria grayi grayi Listeria grayi murrayi Listeria grayi subsp. grayi Listeria murrayi Murraya grayi Murraya grayi subsp. grayi NCBITaxon:1644 NCBITaxon:47986 PMID:1736964 ncbi_taxonomy Murraya grayi subsp. grayi Listeria grayi murrayi Listeria grayi subsp. grayi Listeria grayi grayi Murraya grayi Listeria murrayi Borreliaceae GC_ID:11 PMID:23908650 ncbi_taxonomy Corynebacteriaceae Coryneform bacteria GC_ID:11 PMID:19244447 ncbi_taxonomy Coryneform bacteria Corynebacterium GC_ID:11 PMID:10425754 PMID:19661509 PMID:7547284 PMID:7547291 PMID:7547293 ncbi_taxonomy Corynebacterium diphtheriae Bacillus diphtheriae Bacterium diphtheriae GC_ID:11 Microsporon diphthericum Microsporon diphtheriticum Mycobacterium diphtheriae PMID:7729671 Pacinia loeffleri ncbi_taxonomy Bacterium diphtheriae Bacillus diphtheriae Pacinia loeffleri Microsporon diphthericum Mycobacterium diphtheriae Microsporon diphtheriticum Actinobacteria Actinomycetes High GC gram-positive bacteria Mycobacteriaceae Mycobacterium Mycobacterium Lehmann and Neumann 1896 Mycobacterium leprae Bacillus leprae GC_ID:11 Mycoplasma leprae ncbi_taxonomy Mycoplasma leprae Bacillus leprae Mycobacterium tuberculosis Bacillus tuberculosis Bacterium tuberculosis Mycobacterium tuberculosis typus humanus Mycobacterium tuberculosis var. hominis EEEV complex GC_ID:1 ncbi_taxonomy WEEV complex GC_ID:1 ncbi_taxonomy SFV complex PVC group Mirela L Vasconcelos Terrabacteria group Mirela L Vasconcelos Ebolavirus Ebola-like virus Zaire ebolavirus Reston ebolavirus Ebola virus Reston REBOV Reston Ebola virus Sudan ebolavirus Ebolavirus Sudan SEBOV Sudan Ebola virus Tai Forest ebolavirus CIEBOV Côte d'Ivoire Ebola virus Côte d'Ivoire ebolavirus Ivory Coast ebolavirus Clostridia Mirela L Vasconcelos Clostridiales Mirela L Vasconcelos Peptostreptococcaceae Clostridium cluster XI Mirela L Vasconcelos Bacillaceae Listeriaceae GC_ID:11 PMID:20212322 ncbi_taxonomy Lactobacillales Mirela L Vasconcelos Clostridioides Mirela L Vasconcelos Rift Valley fever phlebovirus Mirela L Vasconcelos Campylobacter Ampylobacter GC_ID:11 PMID:11542086 PMID:12361288 PMID:16627635 PMID:1704793 PMID:19801389 ncbi_taxonomy Ampylobacter Pancrustacea Mandibulata Influenzavirus A Influenzavirus B Mirela L Vasconcelos Coccidioides posadasii GC_ID:1 ncbi_taxonomy Actinobacteria 'Actinobacteria' not Actinobacteria Cavalier-Smith 2002 Spirochaetes GC_ID:11 PMID:11837318 PMID:26654112 Spirochaetae Spirochaetaeota ncbi_taxonomy Spirochaetae Spirochaetaeota Spirochaetia GC_ID:11 PMID:11837318 PMID:25288668 PMID:26654112 Spirochaetes ncbi_taxonomy Spirochaetes Chlamydiae Chlamydaeota Mirela L Vasconcelos Chlamydiia Chlamydiae Mirela L Vasconcelos Neisseriales Mirela L Vasconcelos Fornicata Diplomonadida group GC_ID:1 ncbi_taxonomy Diplomonadida group Helicobacter Mirela L Vasconcelos Helicobacter pylori Campylobacter pylori Campylobacter pylori subsp. pylori Campylobacter pyloridis Helicobacter nemestrinae Mirela L Vasconcelos Campylobacterales Mirela L Vasconcelos SARS coronavirus H5N8 subtype H5N8 subtype of Influenza A virus Brucella Brucella Meyer and Shaw 1920 GC_ID:11 PMID:8573514 ncbi_taxonomy Brucella Meyer and Shaw 1920 Brucella abortus Bacterium abortus Brucella melitensis biovar Abortus Brucella melitensis bv. Abortus GC_ID:11 ncbi_taxonomy Bacterium abortus Brucella melitensis biovar Abortus Brucella melitensis bv. Abortus Cryptosporidium hominis GC_ID:1 ncbi_taxonomy Francisella GC_ID:11 PMID:19783615 PMID:8123561 ncbi_taxonomy Francisella tularensis Bacterium tularense Brucella tularensis Francisella tularense GC_ID:11 Pasteurella tularensis ncbi_taxonomy Brucella tularensis Francisella tularense Bacterium tularense Pasteurella tularensis Metschnikowiaceae GC_ID:1 ncbi_taxonomy Bovinae GC_ID:1 ncbi_taxonomy Alphaproteobacteria Alphabacteria GC_ID:11 PMID:11541974 PMID:11837318 PMID:16166687 PMID:16403855 PMID:19060069 Proteobacteria alpha subdivision Purple bacteria, alpha subdivision a-proteobacteria alpha proteobacteria alpha subdivision alpha subgroup ncbi_taxonomy alpha subgroup Proteobacteria alpha subdivision alpha proteobacteria alpha subdivision Alphabacteria Purple bacteria, alpha subdivision a-proteobacteria Betaproteobacteria Mirela L Vasconcelos Proteobacteria beta subdivision Purple bacteria, beta subdivision beta proteobacteria beta subdivision beta subgroup Porcine epidemic diarrhea virus PEDV Salmonella enterica Bacillus cholerae-suis Mirela L Vasconcelos Salmonella cholerae-suis Salmonella choleraesuis Salmonella enterica ser. choleraesuis Brucella melitensis GC_ID:11 Micrococcus melitensis PMID:8573514 Streptococcus Miletensis ncbi_taxonomy Micrococcus melitensis Streptococcus Miletensis Brucella suis Brucella melitensis biovar Suis Brucella melitensis bv. Suis GC_ID:11 ncbi_taxonomy Brucella melitensis biovar Suis Brucella melitensis bv. Suis Epsilonproteobacteria Mirela L Vasconcelos Proteobacteria epsilon subdivision Purple bacteria, epsilon subdivision epsilon proteobacteria epsilon subdivision epsilon subgroup not Epsilobacteria Spondweni virus group Spondweni virus group Schistosomatoidea Mirela L Vasconcelos Schistosomatidae Mirela L Vasconcelos blood flukes Laurasiatheria GC_ID:1 PMID:11214318 PMID:11214319 PMID:12878460 ncbi_taxonomy Euarchontoglires Simiiformes Anthropoidea Cercopithecoidea Clostridiaceae GC_ID:11 ncbi_taxonomy Tetrapoda tetrapods Amniota Amniota GC_ID:1 amniotes ncbi_taxonomy amniotes amniotes Theria authority: Theria Parker & Haswell, 1897 Sauria Diapsida GC_ID:1 diapsids ncbi_taxonomy Diapsida diapsids Orthoretrovirinae H5N6 subtype H5N6 subtype of Influenza A virus Entamoebidae Entamoebida GC_ID:1 ncbi_taxonomy Entamoebida Opisthokonta Opisthokonta Fungi/Metazoa group GC_ID:1 ncbi_taxonomy opisthokonts opisthokonts Fungi/Metazoa group Onygenales GC_ID:1 Gymnoascales NCBITaxon:259362 NCBITaxon:36053 NCBITaxon:5102 PMID:17486980 ncbi_taxonomy Gymnoascales Metazoa Bilateria Protostomia H7N9 subtype H7N9 subtype of Influenza A virus Neoptera Endopterygota Deuterostomia deuterostomes Carnivora GC_ID:1 carnivores carnivores ncbi_taxonomy carnivores carnivores Alveolata William R. Hogan Matthew Diller alveolates Euglenozoa Euglenozoans Mirela L Vasconcelos Rickettsieae GC_ID:11 PMID:11760958 PMID:8240958 Rickettsieae Philip 1957 (Approved Lists 1980) emend. Brenner et al. 1993 ncbi_taxonomy Rickettsieae Philip 1957 (Approved Lists 1980) emend. Brenner et al. 1993 Francisellaceae Francisella group GC_ID:11 PMID:16280474 PMID:22939414 PMID:26747442 ncbi_taxonomy Francisella group Cryptosporidiidae Cryptosporidae Cryptosporiidae GC_ID:1 ncbi_taxonomy Cryptosporidae Cryptosporiidae dsDNA viruses, no RNA stage dsDNA virus, no RNA stage GC_ID:1 ncbi_taxonomy Retro-transcribing viruses Retroid viruses ssRNA positive-strand viruses, no DNA stage http://purl.obolibrary.org/obo/obi.owl ssRNA positive-strand viruses, no DNA stage ssRNA negative-strand virus dsRNA viruses Mirela L Vasconcelos dsRNA nonenveloped viruses Suina Artiodactyla GC_ID:1 Suiformes ncbi_taxonomy Artiodactyla Suiformes Pecora GC_ID:1 ncbi_taxonomy Equus <subgenus> Equus Equus subg. Equus GC_ID:1 ncbi_taxonomy Equus Equus subg. Equus Rhizobiales GC_ID:11 PMID:16403855 PMID:1854635 Rhizobiaceae group alpha-2 proteobacteria ncbi_taxonomy rhizobacteria Rhizobiaceae group alpha-2 proteobacteria rhizobacteria Plasmodium ovale Matthew Diller malaria parasite p. ovale Streptococcus sp. 'group A' GC_ID:11 Streptococcus sp. (group A) group A streptococci group A streptococcus ncbi_taxonomy Streptococcus sp. (group A) group A streptococci group A streptococcus Brucella canis Brucella melitensis biovar Canis Brucella melitensis bv. Canis GC_ID:11 ncbi_taxonomy Brucella melitensis bv. Canis Brucella melitensis biovar Canis Clavispora GC_ID:1 ncbi_taxonomy Chikungunya virus Haplorrhini Caniformia GC_ID:1 ncbi_taxonomy Rubulavirus GC_ID:1 ncbi_taxonomy Deltavirus Mirela L Vasconcelos Yellow fever virus group GC_ID:1 Yellow fever viruses ncbi_taxonomy Yellow fever viruses Mammalia mammals Plasmodium (Plasmodium) Matthew Diller plasmodium Plasmodium (Laverania) Matthew Diller laverania Culicoidea Aconoidasida Matthew Diller William R. Hogan hematozoa Eimeriorina GC_ID:1 ncbi_taxonomy Enterovirus D68 Dinosauria GC_ID:1 dinosaur dinosaurs ncbi_taxonomy dinosaurs dinosaur Saurischia GC_ID:1 ncbi_taxonomy Theropoda GC_ID:1 ncbi_taxonomy Coelurosauria GC_ID:1 ncbi_taxonomy Culicomorpha Anophelinae GC_ID:1 ncbi_taxonomy Culicinae ssRNA virus Koutango virus GC_ID:1 ncbi_taxonomy Legionellaceae GC_ID:11 Legionellaceae Brenner et al. 1979 PMID:434652 ncbi_taxonomy Legionellaceae Brenner et al. 1979 Anopheles <subgenus> Anopheles GC_ID:1 ncbi_taxonomy Anopheles Legionella GC_ID:11 NCBITaxon:29550 PMID:16166707 PMID:434652 PMID:8573522 PMID:9734026 ncbi_taxonomy Dikarya GC_ID:1 PMID:15689432 PMID:16151185 PMID:17010206 PMID:17051209 PMID:17572334 ncbi_taxonomy Eurotiomycetidae GC_ID:1 ncbi_taxonomy Trichinella britovi GC_ID:1 ncbi_taxonomy Picornavirales Perdicinae GC_ID:1 ncbi_taxonomy Meleagridinae GC_ID:1 ncbi_taxonomy Moraxellaceae Acinetobacteraceae Branhamaceae Mirela L Vasconcelos Acinetobacter Mirela L Vasconcelos Acinetobacter baumannii Acinetobacter genomosp. 2 Acinetobacter genomospecies 2 Bacterium anitratum Mirela L Vasconcelos Fungi GC_ID:1 PMID:11062127 PMID:12684019 fungi fungi ncbi_taxonomy fungi fungi Schizotrypanum Mirela L Vasconcelos Mycobacterium lepromatosis GC_ID:11 PMID:19019760 PMID:25831531 ncbi_taxonomy Neisseriaceae Mirela L Vasconcelos Neisseria "Gonococcus" Lindau 1898 "Merismopedia" Zopf 1885 Gonococcus Mirela L Vasconcelos Neisseria gonorrhoeae Diplococcus gonorrhoeae Gonococcus neisseri Merismopedia gonorrhoeae Micrococcus der gonorrhoe Micrococcus gonococcus Micrococcus gonorrhoeae Mirela L Vasconcelos Neisseria meningitidis Diplokokkus intracellularis meningitidis Micrococcus intracellularis Micrococcus meningitidis Micrococcus meningitidis cerebrospinalis Mirela L Vasconcelos Neisseria weichselbaumii Ascomycota GC_ID:1 PMID:17572334 ascomycetes ascomycetes ncbi_taxonomy sac fungi ascomycetes sac fungi ascomycetes Saccharomycetes GC_ID:1 Hemiascomycetes ncbi_taxonomy Hemiascomycetes Saccharomycetales Endomycetales GC_ID:1 budding yeasts ncbi_taxonomy budding yeasts Endomycetales Candida auris GC_ID:1 ncbi_taxonomy Insecta Alcaligenaceae Mirela L Vasconcelos Chlamydiales Mirela L Vasconcelos Bordetella Mirela L Vasconcelos Bordetella pertussis Bacterium tussis-convulsivae Hemophilus pertussis Microbe de la coqueluche Mirela L Vasconcelos Stegomyia Enterobacteriaceae Enterobacteraceae Mirela L Vasconcelos Salmonella enterica subsp. enterica serovar Paratyphi A Bacterium paratyphi Bacterium paratyphi typhus A Mirela L Vasconcelos Salmonella choleraesuis choleraesuis (serotype paratyphi A) Salmonella choleraesuis subsp. choleraesuis serovar Paratyphi A Salmonella paratyphi Salmonella paratyphi A Salmonella paratyphi-a Herpesvirales GC_ID:1 ncbi_taxonomy Coccidioides GC_ID:1 ncbi_taxonomy Coccidioides immitis GC_ID:1 ncbi_taxonomy Amoebozoa GC_ID:1 PMID:23020233 ncbi_taxonomy Archamoebae GC_ID:1 PMID:23020233 ncbi_taxonomy Escherichia Mirela L Vasconcelos Escherichia coli Bacillus coli Bacterium coli Bacterium coli commune E. coli Enterococcus coli Mirela L Vasconcelos Kinetoplastida Kinetoplastea Mirela L Vasconcelos Protomonadida kinetoplasts Trypanosomatidae Mirela L Vasconcelos Bundibugyo ebolavirus Ebolavirus bundibugyo Trypanosoma Mirela L Vasconcelos Trypanosoma cruzi Mirela L Vasconcelos Diplomonadida GC_ID:1 diplomonads diplomonads ncbi_taxonomy diplomonads diplomonads Hexamitidae GC_ID:6 ncbi_taxonomy Giardia GC_ID:1 ncbi_taxonomy Giardia intestinalis GC_ID:1 Giardia duodenalis Giardia lamblia Lamblia intestinalis PMID:11432808 PMID:19135417 ncbi_taxonomy Giardia duodenalis Giardia lamblia Lamblia intestinalis Entamoeba GC_ID:1 ncbi_taxonomy Apicomplexa William R. Hogan Matthew Diller apicomplexans Coccidia GC_ID:1 coccidians ncbi_taxonomy coccidians Cryptosporidium GC_ID:1 ncbi_taxonomy Cryptosporidium parvum GC_ID:1 ncbi_taxonomy Haemosporida Matthew Diller William R. Hogan haemosporidians haemosporina Plasmodium Matthew Diller Plasmodium falciparum Matthew Diller Mirela L Vasconcelos malaria parasite P. falciparum plasmodium (laverania) falciparum Plasmodium vivax Matthew Diller malaria parasite p. vivax Plasmodium malariae Matthew Diller Salmonella Mirela L Vasconcelos Salmonella enterica subsp. enterica Mirela L Vasconcelos Salmonella cholerae-suis subsp. cholerae-suis Salmonella choleraesuis subsp. choleraesuis Salmonella enterica I Salmonella enterica subsp. I Eumetazoa Platyhelminthes Mirela L Vasconcelos flatworms Trematoda Mirela L Vasconcelos Digenea Mirela L Vasconcelos flukes Strigeidida Mirela L Vasconcelos Schistosoma Mirela L Vasconcelos Schistosoma mansoni Mirela L Vasconcelos Schistosoma haematobium Mirela L Vasconcelos Shigella GC_ID:11 PMID:26834722 ncbi_taxonomy Shigella dysenteriae Bacillus dysenteriae Bacillus dysentericus Bacillus shigae Eberthella dysenteriae Escherichia/Shigella dysenteriae GC_ID:11 PMID:12054222 Shigella shigae ncbi_taxonomy Bacillus shigae Bacillus dysenteriae Eberthella dysenteriae Shigella shigae Escherichia/Shigella dysenteriae Bacillus dysentericus Shigella flexneri Escherichia/Shigella flexneri GC_ID:11 Shigella paradysenteriae ncbi_taxonomy Escherichia/Shigella flexneri Shigella paradysenteriae Nematoda GC_ID:1 Nemata ncbi_taxonomy nematode nematodes nematodes roundworm roundworms roundworm roundworms nematodes nematode nematodes Nemata Shigella sonnei Bacterium sonnei GC_ID:11 ncbi_taxonomy Bacterium sonnei Trichocephalida GC_ID:1 NCBITaxon:36085 NCBITaxon:6331 ncbi_taxonomy Trichinellidae GC_ID:1 ncbi_taxonomy Trichinella GC_ID:1 ncbi_taxonomy Trichinella spiralis GC_ID:1 ncbi_taxonomy Trichinella nativa GC_ID:1 ncbi_taxonomy Trichinella nelsoni GC_ID:1 ncbi_taxonomy Vibrionaceae Mirela L Vasconcelos Zika virus Zika virus Vibrio Beneckea Listonella Microspira Mirela L Vasconcelos Pacinia Arthropoda Vibrio cholerae Bacillo virgola del Koch Bacillus cholerae Bacillus cholerae-asiaticae Kommabacillus Liquidivibrio cholerae Microspira comma Mirela L Vasconcelos Pacinia cholerae-asiaticae Spirillum cholerae Spirillum cholerae-asiaticae Vibrio cholera Vibrio cholerae Pacini 1854 Vibrio cholerae-asiaticae Vibrio comma Giardiinae GC_ID:6 ncbi_taxonomy delta/epsilon subdivisions Mirela L Vasconcelos not Thiobacteria Sedoreovirinae Mirela L Vasconcelos Coronavirinae Alphacoronavirus Coronavirus group 1 Group 1 species Betacoronavirus Hexapoda Pasteurellaceae Mirela L Vasconcelos Diptera Nematocera Culicidae mosquitos Aedes Aedes aegypti Stegomyia aegypti Anopheles <genus> Anopheles GC_ID:1 ncbi_taxonomy Anopheles saccharomyceta GC_ID:1 ncbi_taxonomy leotiomyceta GC_ID:1 ncbi_taxonomy Thiotrichales GC_ID:11 PMID:16280474 Thiomicrospira group Thiothrix/Francisella group ncbi_taxonomy Thiomicrospira group Thiothrix/Francisella group Pseudomonadales Mirela L Vasconcelos Pseudomonaceae/Moraxellaceae group Helicobacteraceae Helicobacter group Mirela L Vasconcelos Campylobacteraceae Campylobacter group Campylobacteraceae Vandamme and De Ley 1991 GC_ID:11 ncbi_taxonomy Campylobacter group Campylobacteraceae Vandamme and De Ley 1991 Haemophilus Mirela L Vasconcelos Haemophilus influenzae Bacterium influenzae Coccobacillus pfeifferi Haemophilus meningitidis Influenza-bacillus Mirela L Vasconcelos Mycobacterium influenzae Pterygota Eucoccidiorida Eucoccidiida GC_ID:1 ncbi_taxonomy Eucoccidiida Rickettsiales GC_ID:11 PMID:11760958 PMID:8240958 Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Brenner et al. 1993 Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Dumler et al. 2001 alpha-1 proteobacteria ncbi_taxonomy rickettsias alpha-1 proteobacteria Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Dumler et al. 2001 Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Brenner et al. 1993 rickettsias Anaplasma Anaplasma Theiler 1910 (Approved Lists 1980) emend. Dumler et al. 2001 GC_ID:11 PMID:11760958 ncbi_taxonomy Anaplasma Theiler 1910 (Approved Lists 1980) emend. Dumler et al. 2001 Nidovirales http://purl.obolibrary.org/obo/obi.owl Nidovirales Chordata chordates Vertebrata authority: Vertebrata Cuvier, 1812 vertebrates Rickettsiaceae GC_ID:11 PMID:11760958 PMID:2592342 PMID:8240958 Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Brenner et al. 1993 Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Dumler et al. 2001 ncbi_taxonomy Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Brenner et al. 1993 Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Dumler et al. 2001 Mycobacterium tuberculosis complex Gnathostomata jawed vertebrates Rickettsia GC_ID:11 PMID:10939649 PMID:11491333 PMID:9103608 Rickettsia da Rocha-Lima 1916 ncbi_taxonomy Rickettsia da Rocha-Lima 1916 Rickettsia rickettsii "Dermacentroxenus rickettsii" Wolbach 1919 Dermacentroxenus rickettsii GC_ID:11 Rickettsia rickettsii (Wolbach 1919) Brumpt 1922 ncbi_taxonomy Dermacentroxenus rickettsii "Dermacentroxenus rickettsii" Wolbach 1919 Rickettsia rickettsii (Wolbach 1919) Brumpt 1922 Rickettsia typhi Dermacentroxenus typhi GC_ID:11 Rickettsia mooseri ncbi_taxonomy Dermacentroxenus typhi Rickettsia mooseri Burkholderiales Burkholderia/Oxalobacter/Ralstonia group Mirela L Vasconcelos Chlamydiaceae Mirela L Vasconcelos Chlamydia Bedsonia Chlamydophila Mirela L Vasconcelos Miyagawanella Rakeia Rickettsiaformis Chlamydia trachomatis Chlamydozoon trachomatis Mirela L Vasconcelos Rickettsia trachomae Rickettsia trachomatis Sarcopterygii Chlamydia psittaci Chlamydia psitacci Chlamydophila psittaci Chlamydozoon psittaci Ehrlichia psittaci GC_ID:11 NCBITaxon:812 PMID:10319462 PMID:12807198 PMID:8102247 PMID:8347519 Rickettsia psittaci Rickettsiaformis psittacosis ncbi_taxonomy Chlamydia psitacci Rickettsia psittaci Ehrlichia psittaci Rickettsiaformis psittacosis Chlamydozoon psittaci Chlamydophila psittaci Sauropsida GC_ID:1 ncbi_taxonomy sauropsids sauropsids Archosauria GC_ID:1 ncbi_taxonomy Corynebacteriales Corynebacterineae Dicondylia Bacillus cereus group Aves GC_ID:1 birds birds ncbi_taxonomy birds birds Neognathae GC_ID:1 ncbi_taxonomy Anseriformes GC_ID:1 ncbi_taxonomy Anatidae GC_ID:1 ncbi_taxonomy waterfowl waterfowl Panarthropoda Craniata Galliformes GC_ID:1 fowls ncbi_taxonomy fowls Phasianidae GC_ID:1 NCBITaxon:9099 ncbi_taxonomy turkeys turkeys Gallus GC_ID:1 ncbi_taxonomy Gallus gallus GC_ID:1 Gallus domesticus Gallus gallus domesticus bantam chicken chickens ncbi_taxonomy Gallus gallus domesticus Gallus domesticus chickens chicken bantam Salmonella enterica subsp. enterica serovar Typhi Bacillus typhi Bacterium (subgen. Eberthella) typhi Mirela L Vasconcelos Salmonella choleraesuis serovar Typhi Salmonella choleraesuis typhi Salmonella enterica ser. typhi Salmonella enterica serotype Typhi Salmonella enterica serovar Typhi Salmonella typhi Phasianinae GC_ID:1 ncbi_taxonomy Coturnix GC_ID:1 ncbi_taxonomy Staphylococcaceae Staphylococcaceae Staphylococcus group Acinetobacter calcoaceticus/baumannii complex Mirela L Vasconcelos Meleagris GC_ID:1 ncbi_taxonomy Meleagris gallopavo GC_ID:1 common turkey ncbi_taxonomy turkey wild turkey turkey common turkey wild turkey Bacilli Bacillus/Lactobacillus/Strptococcus group Firmibacteria Mirela L Vasconcelos Enterobacterales Enterobacteriaceae and related endosymbionts Enterobacteriaceae group Enterobacteriales Mirela L Vasconcelos Cetartiodactyla GC_ID:1 even-toed ungulates ncbi_taxonomy whales, hippos, ruminants, pigs, camels etc. whales, hippos, ruminants, pigs, camels etc. even-toed ungulates Eutheria Placentalia eutherian mammals placental mammals placentals Coturnix japonica Coturnix coturnix Japonicus Coturnix coturnix japanica Coturnix coturnix japonica Coturnix japonica japonica GC_ID:1 Japanese quail ncbi_taxonomy Coturnix coturnix japanica Coturnix coturnix Japonicus Coturnix coturnix japonica Japanese quail Coturnix japonica japonica Anaplasmataceae Anaplasmataceae Philip 1957 (Approved Lists 1980) emend. Dumler et al. 2001 Ehrlichiae GC_ID:11 PMID:11760958 ncbi_taxonomy Ehrlichiae Anaplasmataceae Philip 1957 (Approved Lists 1980) emend. Dumler et al. 2001 Ehrlichia "Ehrlichia (subgen. Cowdria)" Moshkovski 1945 "Kurlovia" Zhdanov 1953 "Nicollea" (in part) Macchiavello 1947 "Nicollea" Macchiavello 1947 "Rickettsia (subgen. Ehrlichia)" Moshkovski 1937 Cowdria Cowdria Moshkovski 1947 Ehrlichia (subgen. Cowdria) Ehrlichia Moshkovski 1945 (Approved Lists 1980) emend. Dumler et al. 2001 GC_ID:11 Kurlovia NCBITaxon:778 Nicollea PMID:11414267 PMID:11760958 Rickettsia (subgen. Ehrlichia) ncbi_taxonomy possibly "Donatienella" Rousselot 1948 Rickettsia (subgen. Ehrlichia) Ehrlichia (subgen. Cowdria) "Rickettsia (subgen. Ehrlichia)" Moshkovski 1937 "Kurlovia" Zhdanov 1953 "Nicollea" (in part) Macchiavello 1947 "Nicollea" Macchiavello 1947 "Ehrlichia (subgen. Cowdria)" Moshkovski 1945 Cowdria Moshkovski 1947 Ehrlichia Moshkovski 1945 (Approved Lists 1980) emend. Dumler et al. 2001 Nicollea possibly "Donatienella" Rousselot 1948 Kurlovia Cowdria Primates Primata primate primates Ehrlichia chaffeensis Ehrlichia chaffeensis Anderson et al. 1992 emend. Dumler et al. 2001 Ehrlichia chaffensis GC_ID:11 PMID:11760958 PMID:1757557 ncbi_taxonomy Ehrlichia chaffensis Ehrlichia chaffeensis Anderson et al. 1992 emend. Dumler et al. 2001 Anaplasma phagocytophilum Anaplasma phagocytophila Cytoecetes bovis Cytoecetes phagocytophila Ehrlichia equi Ehrlichia phagocytophila Ehrlichia sp. 'HGE agent' GC_ID:11 HGE agent NCBITaxon:59888 NCBITaxon:75053 NCBITaxon:75115 NCBITaxon:946 PMID:1115421 PMID:11760958 PMID:8195363 Rickettsia phagocytophila Rickettsia phagocytophila ovis agent of human granulocytic ehrlichiosis human granulocytic Ehrlichia ncbi_taxonomy Ehrlichia phagocytophila Ehrlichia equi Cytoecetes bovis Anaplasma phagocytophila Cytoecetes phagocytophila Rickettsia phagocytophila Rickettsia phagocytophila ovis agent of human granulocytic ehrlichiosis HGE agent human granulocytic Ehrlichia Ehrlichia sp. 'HGE agent' Catarrhini Cercopithecidae Old World monkeys monkey monkeys Cercopithecinae Macaca macaque macaques Macaca fascicularis GC_ID:1 Macaca cynomolgus Macaca irus NCBITaxon:36519 crab eating macaque crab-eating macaque cynomolgus macaque cynomolgus monkey cynomolgus monkeys long-tailed macaque ncbi_taxonomy cynomolgus monkeys long-tailed macaque cynomolgus macaque crab-eating macaque Macaca cynomolgus cynomolgus monkey crab eating macaque Macaca irus Macaca mulatta Rhesus monkey rhesus macaque rhesus macaques rhesus monkeys Canidae GC_ID:1 dog, coyote, wolf, fox ncbi_taxonomy dog, coyote, wolf, fox Canis GC_ID:1 ncbi_taxonomy Canis lupus GC_ID:1 gray wolf grey wolf ncbi_taxonomy gray wolf grey wolf Canis lupus familiaris Canis canis Canis domesticus Canis familiaris GC_ID:1 dog dogs ncbi_taxonomy Canis domesticus dog dogs Canis canis Canis familiaris Perissodactyla GC_ID:1 ncbi_taxonomy odd-toed ungulates odd-toed ungulates odd-toed ungulates odd-toed ungulates Equidae GC_ID:1 horses ncbi_taxonomy horses Equus GC_ID:1 ncbi_taxonomy Equus caballus Equus ferus caballus Equus przewalskii f. caballus Equus przewalskii forma caballus GC_ID:1 domestic horse equine horse ncbi_taxonomy equine Equus przewalskii f. caballus Equus przewalskii forma caballus horse Equus ferus caballus domestic horse Suidae GC_ID:1 NCBITaxon:39423 boars ncbi_taxonomy pigs pigs boars Sus GC_ID:1 ncbi_taxonomy Sus scrofa GC_ID:1 Sus scrofus ncbi_taxonomy pig pigs swine wild boar pigs Sus scrofus wild boar swine pig Ruminantia Artiodactyla GC_ID:1 ncbi_taxonomy Artiodactyla Bovidae GC_ID:1 ncbi_taxonomy Bos GC_ID:1 ncbi_taxonomy oxen, cattle oxen, cattle Bos taurus Bos Tauurus Bos bovis Bos primigenius taurus GC_ID:1 NCBITaxon:272461 bovine cattle cow domestic cattle domestic cow ncbi_taxonomy Bos Tauurus Bos primigenius taurus cattle cow bovine Bos bovis domestic cow domestic cattle Capra GC_ID:1 ncbi_taxonomy Capra hircus Capra aegagrus hircus Carpa hircus GC_ID:1 NCBITaxon:57076 South African angora goat domestic goat goat goats ncbi_taxonomy South African angora goat Carpa hircus Capra aegagrus hircus goats domestic goat goat Ovis GC_ID:1 ncbi_taxonomy Ovis aries GC_ID:1 NCBITaxon:9936 Ovis ammon aries Ovis orientalis aries Ovis ovis domestic sheep lambs ncbi_taxonomy sheep wild sheep Ovis orientalis aries lambs Ovis ammon aries Ovis ovis domestic sheep sheep wild sheep Caprinae GC_ID:1 ncbi_taxonomy contraindication http://purl.obolibrary.org/obo/dideo/dev/dideo.owl A contraindication is a disposition that increases the risk of harm involved in using a particular drug, carrying out a medical procedure, or engaging in a particular activity such that the risk of harm exceeds a threshold. An contraindication serves as a reason to withhold a certain medical treatment. http://en.wikipedia.org/wiki/Contraindication planned process 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) Bjoern Peters Injecting mice with a vaccine in order to test its efficacy We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. branch derived A processual entity that realizes a plan which is the concretization of a plan specification. planned process processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material intervention design http://purl.obolibrary.org/obo/obi.owl An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. OBI branch derived PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study. Philppe Rocca-Serra intervention design data encoding http://purl.obolibrary.org/obo/obi.owl OBI branch derived PlanAndPlannedProcess Branch We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE a documenting process to encode an information entity into a digital document data encoding storage of measurement results from an assay into a text file, such as organization GROUP: OBI PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. organization averaging objective Elisabetta Manduchi PERSON: Elisabetta Manduchi http://purl.obolibrary.org/obo/obi.owl A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. James Malone averaging objective scattered molecular aggregate http://purl.obolibrary.org/obo/obi.owl the sodium and chloride ions in a glass of salt water Collective Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 PERSON: Alan Ruttenberg a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates scattered molecular aggregate data representational model 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009 Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax. GROUP: OBI Melanie Courtot data representational model data structure data structure specification gene regulatory graph model http://purl.obolibrary.org/obo/obi.owl phylogenetic tree protein interaction network center value PERSON: James Malone PERSON: Monnie McGee http://purl.obolibrary.org/obo/obi.owl median median A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. center value average value PERSON: James Malone PERSON: Monnie McGee arithmetic mean average value http://purl.obolibrary.org/obo/obi.owl mean A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. graph of vertices A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix. Bjoern Peters Chris Stoeckert For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities. James Malone WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html graph of vertices http://purl.obolibrary.org/obo/obi.owl device A device is a processed material which is designed to perform some function or functions A voltmeter is a measurement device which is intended to perform some measure function. OBI Vancouver workshop 2010 PERSON: Helen Parkinson device food should not classify as a device - counter example for using manufacturer and not device. macroscopic only if we keep this exploratory term we could reinstate the old device class which is obsolete_device. didn't work before as we had manufacturing as part of the definition. device was needed, but couldn't define in Philadelphia. If we decide that in addition to function there are also capabilities for which a device is created we will include these in the definition. instrument would include reagents computer cluster A group of linked computers, working together closely so that in many respects they form a single computer. PERSON: Erik Segerdell computer cluster http://en.wikipedia.org/wiki/Cluster_(computing) http://purl.obolibrary.org/obo/obi.owl service A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. Carlo; Matt OBI workshop San Diego 2011 http://purl.obolibrary.org/obo/obi.owl providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony service environmental history design MO_698 environmental_history_design Person: Chris Stoeckert, Jie Zheng http://purl.obolibrary.org/obo/obi.owl A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc. environmental history design disease state design Person: Chris Stoeckert, Jie Zheng http://purl.obolibrary.org/obo/obi.owl A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress. MO_902 disease_state_design disease state design pathogenicity design Person: Chris Stoeckert, Jie Zheng http://purl.obolibrary.org/obo/obi.owl A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed. MO_807 pathogenicity_design pathogenicity design data service A service that has some information content entity as input and output. Data analysis service such statistical abalysis or storage service such data backup. Information content entity was used as specified input and output since it was more appropriate then data item or dataset. PERSON: Carlo Torniai PERSON: Carlo Torniai PERSON: Matthew Brush data service http://purl.obolibrary.org/obo/obi.owl rate measurement datum A scalar measurement datum that represents the number of events occuring over a time interval IEDB PERSON: Bjoern Peters, Randi Vita The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time. http://purl.obolibrary.org/obo/obi.owl rate measurement datum investigation description http://purl.obolibrary.org/obo/obi.owl investigationDescription study description A textual entity that describes an investigation. NIAID GSCID-BRC NIAID GSCID-BRC metadata working group Person: Chris Stoeckert, Jie Zheng investigation description project description investigation identifier http://purl.obolibrary.org/obo/obi.owl investigationLabel A CRID symbol used to identify an investigation. NIAID GSCID-BRC NIAID GSCID-BRC metadata working group Person: Chris Stoeckert, Jie Zhneg investigation identifier project ID grant identifier http://purl.obolibrary.org/obo/obi.owl NIAID GSCID-BRC A CRID symbol used to identify a grant. NIAID GSCID-BRC metadata working group Person: Chris Stoeckert, Jie Zheng grant ID grant identifier systematic review study design PERSON: Bill Hogan The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic re\ view. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/ Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/ar\ ticles/PMC4090399/ systematic review study design A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according \ to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were no\ t justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed. digital object identifier http://purl.obolibrary.org/obo/obi.owl Discussed on Aug 22, 2016 OBI dev call. Details see tracker: https://sourceforge.net/p/obi/obi-terms/818/ The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073 https://en.wikipedia.org/wiki/Digital_object_identifier https://www.doi.org/ DOI OBI developers A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles. digital object identifier organism Individual A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. organism data transformation Philippe Rocca-Serra The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. http://purl.obolibrary.org/obo/obi.owl A data transformation is a process which produces output data from input data Branch editors Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing data transformation data transformation objective http://purl.obolibrary.org/obo/obi.owl A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed. James Malone PERSON: James Malone data transformation objective normalize objective averaging data transformation James Malone http://purl.obolibrary.org/obo/obi.owl An averaging data transformation is a data transformation that has objective averaging. PERSON: James Malone averaging data transformation observation design http://purl.obolibrary.org/obo/obi.owl OBI branch derived PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. Philippe Rocca-Serra observation design observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. calculated datum predicted data item BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted. Philippe Rocca-Serra; Bjoern Peters http://purl.obolibrary.org/obo/obi.owl predicted data item A data item that was generated on the basis of a calculation or logical reasoning APOLLO DEVELOPERS: We need to check whether OBI changes the label and the hierarchical place of this class. digital curation Philippe Rocca-Serra http://purl.obolibrary.org/obo/obi.owl wikipedia Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally. PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44. digital curation computer A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. Apple PowerBook, Dell OptiPlex Melanie Courtot Trish Whetzel computer http://en.wikipedia.org/wiki/Computer study design A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert http://purl.obolibrary.org/obo/obi.owl a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design time series design http://purl.obolibrary.org/obo/obi.owl Groups of assays that are related as part of a time series. MO_887 PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources. Philippe Rocca-Serra on behalf of MO time series design software execution http://purl.obolibrary.org/obo/OBIws.owl ITPPR A planned process that realizes the concretization of a software. operation ITPPR web service execution http://purl.obolibrary.org/obo/OBIws.owl web service operation A software execution that is provided by the web service, and involves invoking software execution over network. ITPPR ITPPR clinical finding http://purl.obolibrary.org/obo/ogms.owl A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T10:18:02Z laboratory finding http://purl.obolibrary.org/obo/ogms.owl result Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient. creation date: 2009-06-23T10:21:58Z disease disease A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. Albert Goldfain creation date: 2009-06-23T11:21:20Z http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf disorder http://purl.obolibrary.org/obo/ogms.owl A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. creation date: 2009-06-23T11:39:44Z http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain disease course http://purl.obolibrary.org/obo/ido.owl http://purl.obolibrary.org/obo/ogms.owl disease course The totality of all processes through which a given disease instance is realized. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:55:44Z Albert Goldfain extended organism http://purl.obolibrary.org/obo/ogms.owl Albert Goldfain An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. creation date: 2010-01-25T04:51:11Z http://code.google.com/p/ogms/issues/detail?id=3 treatment Treatment http://purl.obolibrary.org/obo/ogms.owl creation date: 2010-03-31T04:51:11Z http://code.google.com/p/ogms/issues/detail?id=35 A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder Albert Goldfain Apollo-SV currently defines two subclasses of treatment. See vaccination and antiviral treatment. life course LifeCycle http://purl.obolibrary.org/obo/ogms.owl creation date: 2010-03-31T04:51:11Z A processual entity which has as parts all the processes in which a given organism is participant. A processual entity which has as parts all the processes in which a given organism is participant. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=38 health care process http://purl.obolibrary.org/obo/ogms.owl Albert Goldfain creation date: 2011-02-21T09:57:44Z http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process health care encounter http://purl.obolibrary.org/obo/ogms.owl http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter Albert Goldfain creation date: 2011-02-21T09:57:44Z hospitalization hospitalization http://purl.obolibrary.org/obo/ogms.owl Albert Goldfain creation date: 2011-02-21T09:57:44Z http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 TODO outpatient encounter http://purl.obolibrary.org/obo/ogms.owl TODO http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 Albert Goldfain creation date: 2011-02-21T09:57:44Z inpatient encounter http://purl.obolibrary.org/obo/ogms.owl TODO creation date: 2011-02-21T09:57:44Z Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 ED encounter http://purl.obolibrary.org/obo/ogms.owl creation date: 2011-02-21T09:57:44Z http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 Albert Goldfain TODO relapse http://purl.obolibrary.org/obo/ogms.owl A part of a disease course that occurs after an incomplete remission and that is similar to earlier parts of the disease course. http://code.google.com/p/ogms/issues/detail?id=73 Albert Goldfain unique resource locator http://purl.obolibrary.org/obo/omiabis.owl url Mathias Brochhausen http://en.wikipedia.org/wiki/Uniform_resource_locator A CRID that constitutes a reference to an Internet resource. uri human social role http://purl.obolibrary.org/obo/omrse.owl A social role inhering in a human being. Mathias Brochhausen William R. Hogan gender role http://purl.obolibrary.org/obo/omrse.owl sex A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture. Mathias Brochhausen http://en.wikipedia.org/wiki/Gender_role male gender role http://purl.obolibrary.org/obo/omrse.owl A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question. Mathias Brochhausen male gender female gender role http://purl.obolibrary.org/obo/omrse.owl A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question. Mathias Brochhausen female gender human health care role http://purl.obolibrary.org/obo/omrse.owl A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. Mathias Brochhausen William R. Hogan health care role patient role http://purl.obolibrary.org/obo/omrse.owl A human health care role that inheres in an organism [human?] as the recipient of a health care service. A role borne by an organism being as the recipient of a health care service. Amanda Hicks Mathias Brochhausen http://en.wikipedia.org/wiki/Patient patient health care provider organization role http://purl.obolibrary.org/obo/omrse.owl Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division). collection of organisms An object aggregate of organisms. Any arbitrary collection of organisms. They need not be of the same taxonomic class. This term refers to a real population, such as the population of Allegheny County or of the U.S. As a set, it could null (size zero), for example the population of people in Allegheny County older than 130 years of age. It could also be a single organism. The population is not restricted to members of one species. collection of humans http://purl.obolibrary.org/obo/omrse.owl An object aggregate all of whose components are human beings. role in human social processes http://purl.obolibrary.org/obo/omrse.owl A role inhering in an entity realized by social interactions in human society. Mathias Brochhausen Previous definition: A role played by an entity in human social processes. organization social role http://purl.obolibrary.org/obo/omrse.owl A role in human social processes that inheres in an organization. Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants. William R. Hogan organism social role http://purl.obolibrary.org/obo/omrse.owl A role in human social processes that inheres in an organism. Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants. Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc. Previous definition: A role in human social processes played by an organism. William R. Hogan Mathias Brochhausen organization health care role http://purl.obolibrary.org/obo/omrse.owl An organization social role that is realized by a health care process. Previous definition: An organization social role played by an organization in health care processes. aggregate of organizations An aggregate of organizations that have some feature in common, but is not itself an organization. It is often convenient to group organizations together that otherwise might not even interact with one another. William R. Hogan aggregate of sovereign states An aggregate of sovereign states that share some feature in common, but is not an organization nor necessarily the outcome of some treaty among them. William R. Hogan aggregate of geopolitical organizations An aggregate of geopolitical organizations with some feature in common. Examples: all sovereign states whose territory is part of North America, all British Crown Dependencies, all midwestern US States, all US dependencies, etc. William R. Hogan aggregate of dependencies aggregate of major administrative subdivisions hospital function http://purl.obolibrary.org/obo/omrse.owl A function inhering in a facility that manifests by the facility participating in providing inpatient and outpatient healthcare to a patient population. Mathias Brochhausen school function http://purl.obolibrary.org/obo/omrse.owl A function inhering in a facility that manifests by the facility participating in providing formal education to a student population. Mathias Brochhausen hospital role http://purl.obolibrary.org/obo/omrse.owl A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care. Mathias Brochhausen school role http://purl.obolibrary.org/obo/omrse.owl An organization social role that inheres in an organization and is realized by providing formal education to students. Mathias Brochhausen hospital organization http://purl.obolibrary.org/obo/omrse.owl An organization that is the bearer of a hospital role. Mathias Brochhausen school organization http://purl.obolibrary.org/obo/omrse.owl An organization that is the bearer of a school role. Mathias Brochhausen student role http://purl.obolibrary.org/obo/omrse.owl A human social role that is realized by the process of formal education that the bearer undergoes. Mathias Brochhausen nursery school role http://purl.obolibrary.org/obo/omrse.owl preschool Key motivating use case was Synthia synthetic population data. Mathias Brochhausen primary school role http://purl.obolibrary.org/obo/omrse.owl primarySchool Key motivating use case was Synthia synthetic population data. Mathias Brochhausen architectural structure http://purl.obolibrary.org/obo/omrse.owl "Building" is a subclass of this. A material entity that is a human made strcuture with firm connection between its foundation and the ground. Mathias Brochhausen This type of entity is referred to as "Bauwerk" or "Bauliche Anlage". http://de.wikipedia.org/wiki/Bauwerk facility http://purl.obolibrary.org/obo/omrse.owl An architectural structure that bears some function. Mathias Brochhausen hospital facility HealthcareFacility http://purl.obolibrary.org/obo/omrse.owl A facility that is run by a hospital organization and is the bearer of a hospital function. Mathias Brochhausen school facility SchoolFacility http://purl.obolibrary.org/obo/omrse.owl A facility that is run by a school organization and is the bearer of a school function. Mathias Brochhausen secondary school role http://purl.obolibrary.org/obo/omrse.owl secondarySchool Key motivating use case was Synthia synthetic population data. Mathias Brochhausen housing unit houses http://purl.obolibrary.org/obo/omrse.owl A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function. Amanda Hicks Housing units are individuated by their residence functions. https://github.com/ufbmi/OMRSE/wiki/Housing-unit-and-Household household Household http://purl.obolibrary.org/obo/omrse.owl A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of its residence function. Amanda Hicks workplace facility http://purl.obolibrary.org/obo/omrse.owl workplace Amanda Hicks workplace function http://purl.obolibrary.org/obo/omrse.owl Amanda Hicks a function inhering in a material entity that is realized by that material entity being the site where the work of some organization is carried out racial identity datum http://purl.obolibrary.org/obo/omrse.owl race A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method. health care facility http://purl.obolibrary.org/obo/omrse.owl A facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population. identity datum http://purl.obolibrary.org/obo/omrse.owl Amanda Hicks An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method. distance A quality that is the extent of space between two entities. Distance PATO:0000040 http://purl.obolibrary.org/obo/pato.owl quality biological sex biologicalSex http://purl.obolibrary.org/obo/obi.owl An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. biological sex morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. PATO:0000051 http://purl.obolibrary.org/obo/pato.owl quality temperature A physical quality of the thermal energy of a system. PATO:0000146 http://purl.obolibrary.org/obo/pato.owl quality female http://purl.obolibrary.org/obo/obi.owl A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. female male http://purl.obolibrary.org/obo/obi.owl A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. male physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0001018 PATO:0002079 Wikipedia:Physical_property http://purl.obolibrary.org/obo/pato.owl quality relational physical quality physical object quality A quality which inheres in a continuant. PATO:0001237 PATO:0001238 PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. http://purl.obolibrary.org/obo/pato.owl monadic quality of a continuant monadic quality of an object monadic quality of continuant multiply inhering quality of a physical entity quality quality of a continuant quality of a single physical entity quality of an object quality of continuant snap:Quality 1-D extent 1-D size A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. PATO:0001708 http://purl.obolibrary.org/obo/pato.owl quality radius 2012-11-15T05:17:15Z A length quality which is equal to the length of any straight line segment that passes from the center of a circle to any endpoint on the circular boundary. The radius is half of the diameter. PATO:0002390 gkoutos http://purl.obolibrary.org/obo/pato.owl quality radius PCO:collection of organisms A material entity that consists of two or more organisms, viruses, or viroids. Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. May be of the same or different species. group of organisms organism collection population Population A collection of organisms, all of the same species, that live in the same place. ISBN:0878932739 It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across ontologies and only one term used. Still uncertain if this should include every organism of a species living in an area or any subset of them. For now make this a general term (unspecified) and then subclasses can be more specific. collection of organisms of the same species A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. effect size estimate Orlaith Burke http://purl.obolibrary.org/obo/stato.owl AGB,PRS Alejandra Gonzalez-Beltran Philippe Rocca-Serra effect size effect size estimate is a data item about the direction and strength of the consequences of a causative agent as explored by statistical methods. Those methods produce estimates of the effect size, e.g. confidence interval http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/ study group population size Orlaith Burke http://purl.obolibrary.org/obo/stato.owl sampleSize AGB-PRS Alejandra Gonzalez-Beltran Philippe Rocca-Serra statistical sample size statistical sample size is a count evaluating the number of individual experimental units true negative rate Orlaith Burke Alejandra Gonzalez-Beltran Philippe Rocca-Serra specificity specificity is a measurement datum qualifying a binary classification test and is computed by substracting the false positive rate to the integral numeral 1 true positive rate Orlaith Burke Alejandra Gonzalez-Beltran Philippe Rocca-Serra adapted from: http://en.wikipedia.org/wiki/Sensitivity_and_specificity and http://mathworld.wolfram.com/Sensitivity.html recall sensitivity sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1 relative risk Orlaith Burke http://purl.obolibrary.org/obo/stato.owl Philippe Rocca-Serra Relative risk is a measurement datum which denotes the risk of an 'event' relative to an 'exposure'. Relative risk is calculated by forming the ratio of the probability of the event occurring in the exposed group versus the probability of this event occurring in the non-exposed group. Alejandra Gonzalez-Beltran risk ratio categorical variable Orlaith Burke categoricalVariable http://purl.obolibrary.org/obo/stato.owl Alejandra Gonzalez-Beltran Philippe Rocca-Serra http://udel.edu/~mcdonald/statvartypes.html qualitative factor https://onlinecourses.science.psu.edu/stat503/node/7 a categorical variable is a variable which that can only assume a finite number of value and cast observation in a small number of categories discrete variable nominal variable variable Orlaith Burke http://purl.obolibrary.org/obo/stato.owl variable Alejandra Gonzalez-Beltran Philippe Rocca-Serra STATO a variable is a data item which can assume any of a set of values, either as determined by an agent or as randomly occuring through observation. adapted from wolfram-alpha (http://www.wolframalpha.com/input/?i=variable) definition 2. and from Oxford English Dictionary: http://www.oed.com/view/Entry/221514?redirectedFrom=variable#eid, definition B,1 anatomical structure AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:A13 Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome. SCTID:362889002 TAO:0000037 TGMA:0001823 UBERON:0000061 VHOG:0001759 WBbt:0000100 XAO:0003000 ZFA:0000037 biological structure http://dbpedia.org/ontology/AnatomicalStructure http://purl.obolibrary.org/obo/uberon.owl uberon material anatomical entity AAO:0010264 AEO:0000006 Anatomical entity that has mass. BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 UBERON:0000465 VHOG:0001721 http://purl.obolibrary.org/obo/uberon.owl uberon anatomical system AAO:0000007 AEO:0000011 Anatomical group that has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[TAO] Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[AAO] Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[CARO] Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]. BILA:0000011 BSA:0000049 CALOHA:TS-2088 CARO:0000011 EHDAA2:0003011 EHDAA:392 EMAPA:16103 EV:0100000 FBbt:00004856 FMA:7149 HAO:0000011 MA:0000003 NIF_GrossAnatomy:birnlex_14 OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ SCTID:278195005 TAO:0001439 TGMA:0001831 UBERON:0000467 UMLS:C0460002 VHOG:0001725 WBbt:0005746 WBbt:0005763 Wikipedia:Organ_system XAO:0003002 ZFA:0001439 body system galen:AnatomicalSystem http://purl.obolibrary.org/obo/uberon.owl ncithesaurus:Organ_System organ system system uberon tissue AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 Editor note: changed label and definition to reflect CARO2 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:A10 Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. NIF_GrossAnatomy:birnlex_19 TAO:0001477 TGMA:0001844 UBERON:0000479 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 galen:Tissue http://purl.obolibrary.org/obo/uberon.owl ncithesaurus:Tissue portion of tissue simple tissue tissue portion uberon anatomical group AAO:0010008 AEO:0000054 Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue. BILA:0000054 CARO:0000054 EHDAA2:0003054 HAO:0000054 TAO:0001512 TGMA:0001846 UBERON:0000480 VHOG:0001724 XAO:0003001 ZFA:0001512 http://purl.obolibrary.org/obo/uberon.owl uberon immune system AAO:0011003 Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. BILA:0000104 FMA:9825 GAID:328 MA:0002711 MESH:A15.382 OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA SCTID:362590003 TAO:0001159 The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] This class was created automatically from a combination of ontologies UBERON:0002405 UMLS:C0020962 VHOG:0001247 Wikipedia:Immune_system XAO:0003152 ZFA:0001159 http://purl.obolibrary.org/obo/uberon.owl ncithesaurus:Immune_System uberon multicellular anatomical structure An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 UBERON:0010000 http://purl.obolibrary.org/obo/uberon.owl multicellular structure uberon unit http://purl.org/obo/owl/unit unit.ontology unitOfTime dimensionless unit DimensionlessUnit http://purl.org/obo/owl/unit A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. unit.ontology percent Percent http://purl.org/obo/owl/unit A dimensionless ratio unit which denotes numbers as fractions of 100. unit.ontology ratio Ratio http://purl.org/obo/owl/unit unit.ontology A dimensionless unit which denotes an amount or magnitude of one quantity relative to another. fraction Fraction http://purl.org/obo/owl/unit A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator). unit.ontology rate unit Rate http://purl.org/obo/owl/unit unit.ontology A unit which represents a standard measurement occurrence of a process per unit time. vaccine Vaccine http://purl.obolibrary.org/obo/vo.owl Many vaccines are developed to protect against infectious pathogens. Many vaccines are also being developed against some diseases such as cancer and autoimmune diseases. Vaccine is developed against a disease. Allergy. YH, BP, BS, MC, LC, XZ, RS MeSH: D014612 a role that inheres in a prepared material entity that is designed to induce protection or treament for a diease or infection in vivo. A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine. vaccine contraindication VaccineContraindications http://purl.obolibrary.org/obo/vo.owl contraindication for vaccination YH A vaccine contraindication is a contraindication that increases the risks of a vaccination. vaccine function http://purl.obolibrary.org/obo/vo.owl YH, MC, XZ, and AR PERSPN: Oliver He: There has been hot discussion about whether we use 'vaccine function' or 'vaccine role'. Vaccine role may not be the good term to use. Vaccine is designed to be 'vaccine', so it should be vaccine function. One special case is cowpox virus. The cowpox virus can be mixed with some liquid like water and used as a smallpox vaccine. In this case, people often say: the cowpox virus has a 'vaccine role'. However, the cowpox virus vaccine is a processed material of a mix of the virus with water. The virus is a virus, it is not a vaccine per se. Therefore, vaccine role may not be an accurate term. vaccine function is a function that inheres in a vaccine that induces protective immune response against a disease. It is realized in the immunization process in the host. vaccine preparation http://purl.obolibrary.org/obo/vo.owl vaccine production vaccine generation vaccine preparation is a manufacturing process to produce a vaccine. YH, BP obsolete specificity of case detection specificityOfCaseDetection true The specificity of a process or system that detects organisms who satisfy a case definition. 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 deprecated due to malformed URI and created anew. obsolete specificity of treatment detection specificityOfTreatmentDetection true Deprecated due to malformed URI and created anew. William R. Hogan 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 the specificity of the process or system that detects organisms that have undergone a particular treatment obsolete sensitivity of treatment detection sensitivityOfTreatmentDetection true Deprecated due to malformed URI and created anew. William R. Hogan 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 the sensitivity of the process or system that detects organisms that have undergone a particular treatment news article http://purl.org/obo/owl/flybase_vocab Originally imported into Apollo-SV for purpose of indexing in OBC.ide news articles relevant to infectious disease epidemiology. pub_type Bacteria Eukaryota Obsolete Class organism population universal atmosphere of the Earth softwareType administrativeLocations bad_pno_import_4 acknowledgements authors publication Reference bad_pno_import_3 Latitude Longitude CartesianCircleLocationDefinition bad_pno_import_1 bad_pno_import_2 unitOfDistance