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).
National Library of Medicine Identifier
This identifier is the one that the National Library of Medicine uses to identify journals uniquely in PubMed.
NLM ID
linking ISSN
International Standard Serial Number, Linking
The linking ISSN is a single number assigned to all formats of a journal. The online and print versions of a journal, for example, are typically different. The linking ISSN refers to the journal regardless of format.
ISSN Linking
Iso Abbr
ISO Abbreviations are constructed at NLM to assist NCBI in linking from GenBank to PubMed.
ISO Title Abbreviation
The abbreviated journal title assigned by the National Library of Medicine. Typically, it's the ISO title abbreviation without periods.
NLM Title Abbreviation
The date on which a URI annotated with this property was created.
William R. Hogan
This is the date that you created the URI that represents something, NOT the date that the thing referenced by the URI was created. For example, if you create a URI on 2014-09-24 to represent a book published on 1982-10-17, then this annotation property should have the value 2014-09-24. In other words, this annotation refers to the representation, not the represented thing. For the 1982-10-17 date, we suggest the dc:created annotation.
URI creation date
author list
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.
source code version control repository URL
WIlliam R. Hogan
This annotation is intended for annotating instances of software application, software module, ontology (artifact), etc. with a uniform resource locator that points to the source code version control repository where they are managed. Note that for OWL individuals that reference a particular version of the software or ontology, this URL should point to the place in the repository where that version is located, rather than the general main page of the repository.
source code repository URL
human readable synopsis
A comment that summarizes the most relevant or salient features and history of the entity for human readers.
BFO OWL specification label
BFO CLIF specification label
There are several URL and hasURL annotation properties out there in the ontology world. This one had the most sensible source ontology and OBO ID URI combination out there.
hasURL
editor preferred label
editor preferred term
editor preferred term~editor preferred label
example of usage
has curation status
definition
editor note
definition editor
term editor
alternative term
definition source
has obsolescence reason
curator note
imported from
expand expression to
OBO foundry unique label
elucidation
has associated axiom(nl)
has associated axiom(fol)
ISA alternative term
NIAID GSCID-BRC alternative term
temporal interpretation
an alternative term used for STATO statistical ontology and ISA team
Alejandra Gonzalez-Beltran
Philippe Rocca-Serra
STATO alternative term
homology_notes
This annotation property gives the unique label of all Apollo_SV entities that are refered to in the schema. The UAL is the denotator for the Apollo_SV class in the schema. There can at all times only be ONE value of UAL for each class.
Unique Apollo Label
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
Creator
Source
ontology instance unique identifier
ontology IUI
ontology version instance unique identifier
ontology version IUI
label
basis of
p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption.
obsolete is based on
a commissions b, iff a does not participate in the creation or execution of b and participates in a legal agreement that c participates on the creation or execution of b and c getting something in exchange for that participation.
A relation between two entities where the first entity formally requests a third party to create or execute the second entity.
commissions
A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times.
Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222.
instantiates
a simulates b, iff a is a purely intentional entity that is representing a fictional individual or fact b and a participates in a simulating.
simulates
Mathias Brochhausen
causally_precedes
obsoleted_administrated by
has basis in quality
(Q is_a Quality ⋀ D is_a Disposition ⋀ Q base of D) ® ∀q (q instance_of Q ® b (q inheres_in b ⋀ d (d instance_of D ⋀ d inheres_in b)))
Representing dispositions Johannes Röhl and Ludger Jansen Journal of Biomedical Semantics 2011 2(Suppl 4):S4 DOI: 10.1186/2041-1480-2-S4-S4
The relationship between a disposition and the quality that confers the disposition on the material entity in which they both inhere. For example, the disposition of a piece of glass to bend light and the lattice structure of the glass (quality) that results in the bending of the light.
has basis in
obsolete_is_realized_by
Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]
replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by'
realized by
realized_by
is realized by
realizes
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
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
Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte
occurs in
unfolds_in
[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
contains process
is aggregate of
aggregate of
aggregate_of
exists at
the material basis of John’s disposition to cough is the viral infection in John’s upper respiratory tract
the material basis of the disposition to wear unevenly of John’s tires is the worn suspension of his car.
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has material basis at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has material basis@en(x,y,t)'.
b has_material_basis c at t means: b is a disposition & c is a material entity & there is some d bearer_of b at t& c continuant_part_of d at t& d has_disposition b at t because c continuant_part_of d at t. (axiom label in BFO2 Reference: [071-002])
(forall (x y t) (if (hasMaterialBasisAt x y t) (and (Disposition x) (MaterialEntity y) (exists (z) (and (bearerOfAt z x t) (continuantPartOfAt y z t) (exists (w) (and (Disposition w) (if (hasDisposition z w) (continuantPartOfAt y z t))))))))) // axiom label in BFO2 CLIF: [071-002]
has material basis at all times
[copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life
[copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
[copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
[copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
[copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
(iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]
has occurrent part
[copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
has proper occurrent part
[copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
[copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life.
[copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
[copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
[copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
has temporal part
Mary’s 5th birthday occurrent_part_of Mary’s life
The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
the first set of the tennis match occurrent_part_of the tennis match.
[copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001])
occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002])
occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001])
occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001])
occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001])
(forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001]
(forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001]
(forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001]
(forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001]
(forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002]
part of occurrent
proper temporal part of
[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])
(iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001]
proper part of occurrent
the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
the process boundary which separates the 3rd and 4th years of your life.
your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002])
(forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002]
(iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001]
(iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003]
temporal part of
p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
occupies temporal region
[copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
has temporal occupant
during which exists
A pain s-depends_on the organism that is experiencing the pain
a gait s-depends_on the walking object. (All at some specific time.)
a shape s-depends_on the shaped object
one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
the two-sided reciprocal s-dependence of the roles of husband and wife [20
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)
BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
BFO2 Reference: specifically dependent continuant\; process; process boundary
To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001])
If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001])
If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002])
an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002])
if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002])
(forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002]
(forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002]
(forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001]
(forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002]
(forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001]
specifically depends on at some time
has proper temporal part
history of
has history
has measurement unit label
relates a process to a time-measurement-datum that represents the duration of the process
Person:Alan Ruttenberg
is duration of
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
Alan Ruttenberg
has time stamp
relates a time stamped measurement datum to the measurement datum that was measured
has measurement datum
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
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.
owns
a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b.
is owned by
is enrolled in school
is admitted to hospital
bearer of
bearer_of
is bearer of
has_participant
is_concretization_of
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
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].
immediately_precedes
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
A is spatially_disjoint_from B if and only if they have no parts in common
There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
Chris Mungall
Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
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)
negatively regulates
'heart development' has active participant some Shh protein
x has participant y if and only if x realizes some active role that inheres in y
This may be obsoleted and replaced by the original 'has agent' relation
has active participant
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
This relation acts as a join point with BSPO
adjacent to
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporal relation
temporally related to
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
starts with
inverse of ends with
ends
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
finished with
ends with
Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
colocalizes with
causally downstream of
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
causally upstream of
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
obsolete has_disposition
negatively_regulates
NOTE: there appears to be some consistency in usage as to whether processes or continuants realize
obsolete_realized_by
regulates
ObsoleteProperty
obsolete has proper part
a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred from c to a.
A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl
is expressed as
has measurement value
Aedes albopictus
A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an "act") that is laden with determinate, uniformily structured content.
Ingarden, R. (1964) Der Streit um die Existenz der Welt I. Existentalontologie. Max Niemeyer, Tübingen.
Ingarden, R. (1965a) Das literarische Kunstwerk. 3. Auflage. Max Niemeyer, Tübingen.
Ingarden, R. (1965b) Der Streit um die Existenz der Welt II/1. Formalontologie 1. Teil. Max Niemeyer, Tübingen.
Johansson I. (2009) Proof of the existence of universals – and Roman Ingarden's Ontology. Metaphysica. International Journal for Ontology & Metaphysics. 10, 65-87
Thomasson AL. "Ingarden and the Ontology of Cultural Objects." In: Chrudziminski A (ed.): Existence, Culture, and Person. The Ontology of Roman Ingarden. Frankfurt: ontos, 2005, 115-136.
MB: Right now we represent 'purely intentional entities' as siblings to 'information content entities'. Given their nature I am not entirly sure that this is correct. It seems that both 'information content entity' and 'simulation' are subclass to 'purely intentional entity'.
purely intentional entity
A disease transmission model whose concretization is realized as a simulation of infectious disease epidemic or infectious disease pandemic.
An algorithm the concretizations of which models the transmission of transmissible disease.
epidemic model
The average number of transmissions of an infectious agent from an infectious organism to a susceptible organism within a completely susceptible population.
The number of organisms that each infected organism infects in a completely susceptible population during its infectious period.
MB: Here we run into the well know DL problem that we cannot specify that the infectious agent that is transmitted is of the same type that the infectious agent the population is susceptible to.
basic reproduction number
A population survey that assesses the level of immunity against a particular pathogen in a specified population.
Comment from Mike (to do!): I checked because an infection and immunity census would involve two different census methods. One would be some kind of disease surveillance that counts infections. The other is some kind of immunity census process based on seroprevalence studies or vaccination registries.
population immunity survey
a planned process that (1) has at least one process part that has as participants representations of participants (in place of those participants) of processes of type X, and where all such process parts substitute for parts of processes of type X, and (2) is carried out for the purpose of planning for processes of type X, learning more about processes of type X, or teaching about processes of type X.
A process that replaces the essential participants of another type of process with representations of those participants.
For example, in a simulated volcano eruption, representations of lava, lava tubes, vents, etc. take the place of actual lava, lava tubes, vents, etc. Even in the case of a simulated disaster scenario where actual ambulances, fire trucks, and people participate, representations of catastrophic events and injuries, etc. take the place of real ones.
simulating of process of type X
An identifier that refers to the legal person that commissions a simulation process.
An identifier that refers to the person or organization who is requesting one or more executions of the simulator software.
Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.
simulation requester identifier
A software application that provides a model of a real phenomenon based on a set of mathematical formulas.
simulation software application
A planned process resulting in a software product involving the creation of source code.
software development
An identifier that refers to the legal person that creates and maintains a simulator.
An identifier that refers to the person or organization who is responsible for the simulator. It is intended to uniquely identify a person or organization. That said, we do not plan to control the namespace for simulator developer at this point in development. We will add our ideas about alternatives at a future date.
simulator developer identifier
An identifier that refers to all version of a specific simulator.
An identifier that refers to all versions of a specific simulator, such as “FRED”. We intend that it uniquely identify a simulator when combined with simulator developer. For example, the combination www.psc.edu/FRED would differentiate the FRED simulator created by a Pittsburgh organization from another “FRED” simulator maintained elsewhere. The implementation of namespace control for simulator name (i.e., making sure that they don’t use “FRED” twice) is the responsibility of simulator developer.
simulator identifier
A control strategy start time information item that is based on a condition that triggers the control strategy.
control strategy reactive start time information
A numeral that is part of a simulation time step action specification.
A number of time step units in a time step of a simulation. For example, if the time step is 6 hours, then this value is 6.
simulation time step value
An identifier that, as part of a complete simulator identifier, refers to one specific version of a simulator software.
An identifier that refers to a unique version of a simulator. Simulator version distinguishes, for example, version “2.0” from “2.0.b”
simulator version identifier
A time unit that is part of a simulation time step action specification.
A unit of time for each time step of a simulation, such as “hours” or “days”.
simulation time step unit
The action specification that specifies the number of time steps a simulation is going to run.
The number of time steps in a simulator run. For example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero.
simulation run length
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.
infectious period duration
A duration of the time interval between the host acquiring an infection and the host bearing a contagiousness disposition during the same disease course within a population of hosts.
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.
latent period duration
count of simulated susceptible population
count of simulated exposed population
count of simulated contagious population
count of simulated resistant population
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.
MW: I know this causes problems with our set-theoretic definition. Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step. Any ideas? I’ve considered and rejected allowing individual organisms to be fractional. Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’
count of simulated population
An action specification comprising the number of doses and their timing for a vaccination of an individual organism against a specific infectious agent.
A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism.
vaccination dose schedule
The fraction expressing the probability that an organism who is eligible according to a particular vaccination policy will be consented for that vaccination.
The fraction of individuals in a population who are eligible according to a particular vaccination policy and will accept vaccination assuming no supply constraint.
MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class "eligibility rule" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.
MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy” and “control measure efficacy delay.” We could then post-coordinate particular control measures such as vaccine. It is worth noting that there are control measures such as closing schools that are not applied at the individual level. We have not represented those control measures yet.
vaccination compliance
The infectious disease treatment efficacy of a vaccine.
The degree to which a particular vaccination reduces the probability that a vaccinated individual will have a particular vaccination preventable outcome.
Notes: 1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’ 2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer
need to generate class restriction. Something like: 'is realized by' some (processual_entity and (has_participant some ('Anatomical structure' and ('is physical basis of' some 'protective resistance')) we'd also like to say that the protective resistance disposition began to exist during the process. can't recall whether we should use process or processual_entity for future BFO compatibility.
vaccination efficacy
A planned process involving counting numbers of facilities in a specific region.
facility survey
Motivating use case is Synthia synthetic population data.
school facility census
A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.
infectious disease control strategy execution
Key motivating use case was Synthia synthetic population data.
hospital patient population
A simulation of a population or populations of organisms of a particular biological taxon that simulates a particular type of event or types of event that occur in a specified time interval.
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)
simulated population
simulation of population
A measurement datum that is the output of counting.
count
The planned process of finding the number of elements in a finite set of objects.
counting
simulation of organism
A continuous parametric probability distribution that is uniform; centered around the mean, parameter μ​; and whose spread of standard deviations, parameter σ​, adheres to the empirical rule.
A continuous probability distribution in which the parameter μ is the mean or expectation of the distribution and the parameter σ is its standard deviation
normal distribution
A simulation of an infectious agent host that is not contagious and is part of a simulated population.
A simulated organism in a simulated population that has acquired a particular simulated disease but is not yet able to transmit the disease to another simulated organism.
simulation of exposed organism
An identifier that refers to a geographical location to be used as location of a population in a simulation.
An identifier referring to geographical location of a simulated population. Our intent is for the location identifiers to be INCITS codes.
simulated population location identifier
A simulation of an infectious organism host that is contagious.
A simulated organism in a simulated population that has acquired a particular simulated disease and is able to transmit the disease to another simulated organism.
simulation of infectious organism
A simulated organism in a simulated population that is not susceptible.
A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. Note that the name for this concept, were it to be named based on its intent, would be ‘immune.’ However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’ The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage.
simulation of recovered organism
A representation of a disposition realized in a represented disease course that at least part of the simulated population is represented as participating in.
The disease being simulated.
simulation of disease
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.
reproduction number
nursery school student population
The fraction given to express the probability that an organism will become infected, but stay asymptomatic.
The fraction of infectious individuals who do not develop symptoms during the course of their infections.
obsolete_asymptomatic infection fraction
An action specification giving the number of doses of vaccine to be made available over a specific time period.
The counts of vaccine doses that become available in a specific population location during (at the start of would be unambiguous) each simulator time step.
vaccine supply schedule
An action specification giving the number of vaccinations possible in a population during a specific time interval.
The counts of individuals that could be vaccinated in a population location per time step unit in the absence of any vaccine supply constraints. It represents the capacity of medical system to vaccinate individuals.
vaccination administration capacity
The infectious disease treatment efficacy of an antiviral drug.
The degree to which a particular antiviral drug reduces the probability that a treated individual will have a particular preventable outcome. Preventable outcomes include but are not limited to infection, infectiousness, symptoms, and hospitalization.
MB: For DL reasons the easiest way to formalize the definition was to assume only organism that are either host or not immune undergo antiviral treatment. Is that adequate? I assume this'll create problems…
antiviral treatment efficacy
The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role.
The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection.
antiviral efficacy delay
The fraction expressing the probability that an organism will be consented to receive antiviral treatment when eligible.
The fraction of individuals in a simulated population that will accept antiviral treatment if offered.
MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for an antiviral treatment against the members that are eligible and consented the antiviral treatment. There is a class "eligibility rule" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.
MW: Since the estimates that modelers use are from real populations, I have two questions: 1. Should we distinguish between real and simulated population? 2. If so, do we want to represent a ‘measured’ antiviral compliance number that is a property of a real population and distinguish it from this number that we are using to study what might happen in a simulated population? MB: This issue will need to be taken care of in the axiomatization of simulated population
antiviral compliance
An action specification giving the number of doses of an antiviral to be made available during a specific time interval.
Counts of antiviral doses that become available in a specific location per time step unit.
antiviral supply schedule
An action specification that tells the total number of antiviral doses available to be administered to a population during a specific time interval.
Counts of antiviral doses that can be administered in a specific location per time step unit.
antiviral administration schedule
A simulated organism that is assumed “eligible, willing and able” to participate with a particular control measure.
A simulated organism in a simulated population that is “eligible, willing and able” to participate with a particular simulated control measure.
MB: APOLLO_SV_00000053 and APOLLO_SV_00000058 have not been given a class restriction, since they are not expressible in BFO right now, due to their referring to "will". Both classes have been made disjoint in the OWL file, though.
This class will need more ontological reasoning, since the "willing" part of the definition is not representable in BFO to date.
simulation of organism awaiting control measure
An identifier that refers to a specific simulator.
The combination of simulator developer, simulator name, and simulator version, for example “www.psc.edu/FRED/2.0” The combination is intended to uniquely identify the simulation algorithm that produced output X, given input Y to support scientific audit, error analysis, and reproducibility of results.
MB: I am not 100% happy with the elucidation. Can't we just say that this is the full identifier identifying the simulator with both its name and its version number?
complete simulator identifier
A simulating of a disease epidemic or pandemic.
the process of simulating a disease epidemic or pandemic. This term is not currently used in Apollo-WS.
epidemic simulating
Motivating use case is to cover Synthia data, and possibly configuration/output of the MRSA simulator in the MIDAS community (CA-MRSA Repast).
hospital patient population census
A simulated organism that is assumed “ineligible, unwilling or unable” to participate with a particular control measure.
A simulated organism in a simulated population that is “ineligible, unwilling or unable” to participate with a particular simulated control measure.
This class will need more ontological reasoning, since the "unwilling" part of the definition is not representable in BFO to date.
simulation of organism not awaiting control measure
A simulated organism that participates in a particular control measure that has not yet been effective.
This concept represents a simulated organism that has received a control measure such as vaccination in which a period of time must elapse before the benefit of the control measure accrues. A simulated organism is ‘awaiting efficacy’ if ‘efficacy delay’ (e.g. the concept ‘antiviral efficacy delay’ for the particular simulated control measure is greater than the elapsed time between application of the control measure and the current simulated time.
simulation of organism awaiting effect of control measure
The simulation of an antiviral control measure.
A type of control measure based on administration of chemotherapeutic agents to an infected or high-risk organism that kill or inhibit replication of viruses within a simulated organism.
MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI). AND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess. Maybe we need to discuss this.
simulation of antiviral control measure
A simulation of a vaccination control measure.
A type of control measure that uses vaccination to create immunity in simulated organisms to specific pathogens.
simulation of vaccination control measure
primary school student population
A simulation of an organism in a simulated population that has participated in an epidemic control measure.
A simulated organism in a simulated population has participated in a particular simulated control measure. (e.g. an organism received antiviral treatment)
simulation of control measure participant
A time sampled measurement data set, where the position in the sequence of each data item corresponds to a specific time_step of the simulation.
A sequence of data points, where the position in the sequence of each data point corresponds to a specific time_step of the simulation.
MB: The ontological status of simulations (Thoughts) One property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating. While in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.
simulation time series
A numeral that indexes a specific simulation.
The run id indexes a run of a specific simulator version on a specific simulated population, disease(s), and optionally control measures. The simulator is responsible for generating a run id and ensuring its uniqueness.
Class was originally created to correspond with an element from Apollo XSD v3.1.0.
simulation identifier numeral
A purely intentional entity that simulates a temporal interval of pre-specified length.
simulation of time step
An action specification that specifies the length of the time steps interval assumed in a simulation.
simulation time step value simulation time step unit simulation run length The time step value and unit are specified using a scalar value specification.
simulation time step action specification
A numeral that indexes a specific time step of a simulation.
The time step number of a simulation.
time step identifying numeral
A purely intentional entity that simulates an entity and its properties.
simulation
The simulation of geographical location in which a population is assumed to be located.
obsolete_simulation of population location
A simulation of a susceptible organism in a simulated population.
A simulated organism in a simulated population that is capable of acquiring a particular simulated disease.
simulation of susceptible organism
A simulation of a symptomatic infectious agent host.
A simulated organism in a simulated population that has at least one symptom caused by a particular simulated disease.
simulation of symptomatic organism
A simulation of an asymptomatic infectious agent host.
A simulated organism in a simulated population that has no symptoms caused by a particular simulated disease.
simulation of asymptomatic organism
An objective specification that is realized by processes that are able or likely to stop the spread of a disease in a population.
an objective of achieving satisfactory control of epidemic spread through a population
typically, the process endpoint is achievement of R0 < 1
infectious disease control objective specification
the mean or expectation of a distribution
standard deviation
beta distribution
a continuous probability distribution over variable X whose parameters denoted μ and σ are, respectively, the mean and standard deviation of the variable’s natural logarithm
deprecated log normal distribution
A continous probability distribution whose parameters a and b, denote its minimum and maximum values
uniform distribution
a continuous probability distribution with lower limit a, upper limit b and mode c, where a < b and a <= c <= b.
triangular distribution
a discrete probability distribution
Bayesian network
a discrete probability distribution that conditions on time
temporal Bayesian network
An action specification comprising the number of doses and their timing for administering a substance to an individual organism to prevent the negative effects of a specific infectious agent to that organism.
A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism.
control strategy dose schedule
age structure data set
A data set consisting of measurements of age organized in age brackets.
age data in age brackets data set
A plan specification whose objective specification is an infectious disease control objective specification.
A plan with the goal of preventing or mitigating the effects of infections in a population due to one or more pathogens.
The essential goal of an infectious disease control strategy is to protect the susceptible organisms in a population.
infectious disease control strategy
The count of individuals in a susceptible population (empirical or virtual).
count of susceptible population
The count of individuals in an exposed population (empirical or virtual).
count of contacted population
A measurement datum that is about a vaccination efficacy and is the specified output of a vaccination efficacy study.
A vaccination efficacy that results from a vaccination efficacy study.
1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’ 2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.
measured vaccination efficacy
a study design execution that has as its specified output one or more measured vaccination efficacy data items
an experiment that measures vaccination efficacy from a sample of vaccinated and possibly unvaccinated individuals
vaccination efficacy study design execution
an organism that has the property of being immune to a specific disease agent
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%
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.
Two or more distinct populations that are part of the same biotic ecosystem.
community
a probability distribution over a discrete random variable
deprecated discrete probability distribution
The increments of measurement for a measurable thing
obsolete unit of measure
The sum of all biotic and abiotic entities in a geographical region.
ecosystem
The count of individuals in a contagious population (empirical or virtual).
count of contagious population
The count of individuals in a resistant population (empirical or virtual).
count of resistant population
The abiotic ecosystem is the sum total of all continuants in a geographical region that are not organisms, parts of organisms, or dependent continuants that inhere in organisms.
abiotic ecosystem
An action specification that is part of a simulation software and specifies the time step numeral identifying the time step after which a simulation of a control strategy starts.
The number of time steps after which a control strategy starts in a simulator.
fixed control strategy start time specification
A rule that is part of an infectious disease control strategy specification and specifies at which fraction of a population a control strategy is to be discontinued.
A fraction of a population that is targeted for treatment at which the control strategy is discontinued. The concept derives from the epidemiological notion of ‘herd immunity,’ which is a level of immunity in a population at which there are not enough susceptible individuals for a contagious disease to maintain the chain reaction. Technically, it is when the effective reproduction rate <= 1, which means that infectious individuals at most infect one person during the course of their illness.
control strategy reactive endpoint fraction
The biotic ecosystem is the sum total of all organism populations in a particular geographical region.
biotic ecosystem
An identifier that refers to the legal person that creates and maintains software.
software developer identifier
An identifier that refers to a specific piece of software.
complete software identifier
a fiat object part that is in gaseous phase and that is the outer layer of an object in space and is held to the object by gravitational force
atmosphere of Earth, Earth's moon, Saturn, Titan, etc.
outer, gaseous layers of exoplanets are called extraterrestrial atmosphere.
atmosphere
An identifier that, as part of a complete software identifier, refers to one specific version of the software.
software version identifier
An identifier that refers to all version of a specific software.
software identifier
atmosphere of geographical region
An educational institution is an place organization which provides the necessary system for people of different ages gain an education. It includes (among others) preschools, childcare, elementary schools, and universities.
http://en.wikipedia.org/wiki/Types_of_educational_institutions (amended)
obsolete_educational institution
An information content entity about educational institutions that is part of the action sepcification of a school closure control measure.
The specification of which facilities to target in a school closure control measure.
school closure target facilities
A reproduction of a pathogen organism of a particular biological taxon in a tissue of a host organism from another taxon.
infection process
process of infection
A process of reproduction of a particular pathogen species inside some tissue of a particular host species.
M. Brochhausen
infection is reproduction of a pathogen inside some tissue of a host. By associating infection with the classes latent period and infectious period, which are associated with specific pathogen species and host species, Apollo-SV defines infection further as reproduction of a particular pathogen taxon inside some tissue of a particular host taxon.
infection
The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources
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
infection acquisition
An identifier that refers to a type of vaccine, i.e., one of a class of manufactured vaccines that public health would consider interchangable.
A unique identifier for a vaccine.
vaccine identifier
latent period
a unique identifier that refers to a protocol for vaccinating one person
A unique identifier for a vaccination protocol (the process of vaccinating one person)
vaccination identifier
the number of doses of vaccine that are recommended to achieve immunity
vaccination course
an interbreeding population
species
a unique identifier that refers to an antiviral drug product
A unique identifier for an antiviral drug
antiviral identifier
A place closure control strategy whose action specification is realized in a school closure process.
A control measure in which schools are closed in an attempt to reduce transmission of disease.
school closure control strategy
The number of time steps that a school closure control measure prescribes that schools will remain closed.
school closure duration
The time steps that a school will be in session.
school calendar
Faciilities that are the target of a control strategy
control strategy target facilities
A simulated population that is the target of a control strategy and its priority under triage conditions
control strategy target populations and prioritization
Fraction of organisms in a target population that a control strategy program seeks to enroll or prioritize
a specification of a population that a control strategy applies to. It is intended to apply to a real population, so I don’t know whether you would consider it a simulated thing. I don’t.
control strategy target population fraction
an epidemic control measure plan specification that has a conditional specification as part
a control measure (program) that is initiated or modified by an epidemic-related event (or if you prefer, an event occurring within/during the simulation)
obsolete_Reactive control measure
An event in the ecosystem that triggers the starting or stopping of a control strategy.
reactive control strategy test
A data item that specifies the fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.
A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy. The event could be infection acquisition, vaccination, antiviral treatment, etc.
reactive control strategy threshold
secondary school student population
A measurement datum of the time interval from the decision to implement an infectious disease control strategy to the start of the control strategy expressed in number of time intervals.
A period from the initiation of a control strategy until its disease-controlling actions actually begin. For example, once a vaccination control strategy starts, individual vaccinations may not occur right away: it might take some time until workers and vaccines are deployed and ready to begin.
control strategy response delay
Number of time steps it takes medical personnel to ascertain a symptomatic individual from onset of symptoms
per Mike Wagner, this is input
ascertainment delay
Fraction of all symptomatic individuals who will be ascertained
fraction of organisms (usually infected) that a surveillance system detects out of the total population
ascertainment fraction
An individual treatment control strategy that has as part an action specification that is realized in a vaccination process.
An individual treatment control strategy that administers one or more vaccines to individuals in a population with the goal of inducing resistance to infection with a particular pathogen in those individuals.
vaccination control strategy
the number of distinct antigenic strains in a vaccine product
vaccine valence
An action specification that tells how many doses of antiviral drug should be given to each individual that participates in the antiviral control measure.
The quantity of antiviral drug used to treat one individual
antiviral course
A measurement datum about the fraction of individuals in a population that elect to participate in a control strategy when offered.
A fraction of eligible individuals in a population who receive an intervention or participate in a control strategy.
the class restriction can be made more precise AH
the fraction of some population that is targeted for a control strategy that accepts it. It can obviously also be interpreted as a probability that the average individual in the targeted population accepts/complies with the control strategy. It is not simulated
control strategy compliance
infectious period
protect against effect of pathogen
A treatment that consists of the administration of antigenic material to stimulate an individual's immune system to develop adaptive immunity to a pathogen.
A treatment of an individual with antigenic material from a pathogen that has the goal of inducing resistance of the individual to infection with the pathogen.
vaccination
replaced with VO 'vaccine function'
vaccine disposition
disposition to become contaminated with a pathogen
The dispostion of an organism of a particular biological taxon A that is realized by inhibiting the establishment of an infection by an organism of another particular biological taxon that bears an infectious disposition towards members of A
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.
resistance to infection
Transmission parameter (sometime known as Ptrans). This value is multiplied by the inter-personal contact probability to determine the transmission probability between infected and susceptible persons.
it is the same thing as transmission coefficient
beta
Transmission parameter
inter-personal contact probability
random number seed
A number between 0 and 1 indicating the degree of susceptibility of an organism
susceptibility measurement datum
a fraction of the target population, that once vaccinated, results in stopping further vaccination in the population
vaccination reactive end point fraction
Resistance to infection that is conferred by immune system/immune mechansisms.
immune resistance to infection
A planned process involving counting numbers of a organism population, possibly including counting sub-populations fulfilling specific criteria.
population survey
A census that is the outcome of a population survey.
population census
A population of host organisms undergoing infection and that are not infectious.
exposed population
A population survey that counts the number of individuals in the population who are infected with a particular pathogen.
Equivalent class was: 'population survey' and (has_part some (counting and (has_specified_output some (count and ('is about' some 'exposed population'))) and (has_specified_output some (count and ('is about' some 'infectious population'))) and (has_specified_output some (count and ('is about' some 'susceptible population'))) and (has_specified_output some (count and ('is about' some 'immune population')))))
population infection survey
A population of host organisms undergoing infection that are contagious.
contagious population
A census that is the result of a population infection survey and a population immunity survey.
PII Census
A census of the infection status (e.g., susceptible, infected, infectious, and immune/resistant) of organisms in a population, with respect to a particular pathogen.
population infection and immunity census
population demographic survey
A census that is the specific outcome of a population demographic survey.
population demographic census
obsolete_contamination
An ecosystem in which a population of hosts is undergoing at least one infection.
MIDAS scenario
An information content entity that is about a MIDAS scenario and contains population disease census data.
need to change the text definition. need to change label to be more consistent with current Apollo terminology (possibly 'infectious disease scenario'.
MIDAS scenario representation
A population of organisms that have been infected, but are no longer able to transmit the disease and to acquire the infection again.
recovered population
synthetic ecosystem constructing
A planned process that has one or more synthetic ecosystem datasets as output.
creating a synthetic ecosystem dataset
synthetic ecosystem generating
agent-level ecosystem data generation
A census that is the specified output of a agent-level ecosystem data generation that had census data as an input.
agent-level ecosystem census
An independent continuant that is the localization of a pathogen, but is not undergoing an infection.
A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.
contaminated thing
A biological process whereby an entity that is not in contact with a pathogen of a particular biological taxon begins to undergo contamination with that pathogen.
contamination acquisition
nursery school student population census
primary school student population census
secondary school student population census
A treatment with an antiviral drug.
A treatment of a particular host with a particular antiviral drug with activity against a particular viral pathogen.
antiviral treatment
The ability to participate in infection acquisition as a host.
susceptibility
A data set of a specific entity in a specified region at a specified time.
census
An algorithm that models the progress of a transmissible disease in a population.
disease transmission model
An organization created with the purpose of providing education to those of its members that are bearer of student role.
obsolete_school organization
school student population census
The collection of students administrated by exaclty one school organization.
school student population
An information content entity that contains everything a simulator needs to run, including the representation of a scenario.
simulator configuration
A human social role that is realized by attending a school to receive formal education.
obsolete_student role
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.
antiviral control strategy
contagiousness
An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps).
simulator time specification
A dataset that represents at least one pathogen population (of a particular biological taxon) in one host population (of a particular biological taxon) in an ecosystem in a particular location at a particular point in time.
Data about an infection in an ecosystem at a specific location and 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.
infectious disease scenario
An identifier that denotes a real date corresponding to simulator time zero.
A reference to the date that corresponds to simulator time zero.
scenario date
biological contamination
The process of existence without reproduction of a pathogen of a particular biological taxon in or on some material entity or the process of reproduction of a pathogen in or on a material entity that is not an organism.
the preferred term is biological contamination to distinguish from things like radiological contamination, contamination of the Gulf of Mexico with oil, the contamination of air with pollution, etc.
contamination
A census about a particular medical treatment of a population.
A census of a population that determines for a particular treatment whether each organism in the population has undergone that treatment.
population treatment census
A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero.
This census should exclude infection, immunity, treatment, or contamination.
population and environment census
A census that is the outcome of assessing control-strategy-related facilities and supply chains.
control strategy inventory census
A host who is able to transmit some infection to another organism.
An infected organism of a particular species who is able to transmit the infection to a susceptible organism of a particular species. Note that the infected and susceptible organisms may be of different species.
contagious organism
An information content entity that represents the rate that an infection moves from infected individuals to susceptible individuals in a population.
transmission coefficient
A data item specifying a measured vaccination efficacy.
obsolete vaccination efficacy measured
A data item inferring a vaccination efficacy based on epidemiological data.
vaccination efficacy inferred
vaccination control strategy, antiviral control strategy
An infectious disease control strategy that immediately targets individuals.
individual treatment control strategy
An organism population that is the target for a disease control strategy.
target population
ring vaccination individual treatment control strategy
An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved.
agent level population and environment census
At present, this class corresponds with an XSD type that contains authentication plus information needed to generate a Synthia synthetic population dataset including (1) geographical location and (2) a list of household characteristics.
agent model ecosystem census description
The Apollo XSD allows us to specify counts of certain subpopulations and abiotic ecosystem elements for a compartmental model (vs. specifying each individual in the population as in agent model population and environment census).
compartment model population and environment census
population strata definition
A census about contaminated things of a given type in an area of interest.
contaminated thing census
A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved.
indexable Apollo item
A taxonomy identifier curated by the NCBI Taxonomy that designates a biological taxon.
An identifier curated by the National Center for Biotechnology Information (NCBI) that designates a particular biological taxon (e.g., Homo sapiens).
NCBI taxon identifier
A processual entity that is either the outcome of a disease course or a part of a disease course and has etiological relevance.
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),
disease outcome
An organism that is the bearer of a susceptibility disposition.
An organism of a particular species that can undergo infection with a particular pathogen.
susceptible organism
An organism that is the bearer of an immune resistance disposition.
An organism of a particular species that has developed immune resistance to infection with a pathogen of a particular species.
immune organism
an organism that is the bearer of resistance to infection
An organism of a particular species that is unable to undergo infection with a particular pathogen.
resistant organism
An information content entity that specifies the start time of the implementation of a infectious disease control strategy.
A specification of when an infectious disease control strategy starts.
control strategy start time information
organism in latent period of infection
An infectious agent host who is NOT able to transmit the infection to another organism of the same species.
An infected organism of a particular species that is not yet able to transmit the infection to a susceptible organism of a particular species. Note that the infected and sucseptible organisms may be of different species.
infected organism
A simulator configuration that start an Apollo simulator.
apollo simulator configuration
The probability of the occurence of an infection acquisition from one infected organism to another when in contact.
transmission probability
A plan specification that specifies the capacity to administer a particular treatment over a specific temporal interval in a specified geographical region.
A specification of how many doses (of material) of an individual treatment can be administered per unit time in a particular geographical location.
treatment administration capacity schedule
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.
treatment supply schedule
An information content entity that specifies the vaccination efficacy that is part of a simulator configuration.
vaccination efficacy for simulator configuration
An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference.
probability distribution
discrete probability distribution
A data item that specifies the epidemiologically-relevant state of a host organism at a specific time with respect to infection with a particular pathogen.
infection state data item
An objective specification that specifies the disease outcome a vaccination seeks to prevent.
vaccination preventable outcome
An information content entity that designates a biological taxon and optionally a clade of pathogens.
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.
Apollo pathogen code
A material entity that is part of an abiotic ecosystem.
abiotic ecosystem element
An immune population that acts as the members know they are immune (do not seek vaccination/antiviral treatment, etc.).
immune population acting like immune
An immune population that acts as the members assume they are not immune (e.g. seek vaccination/antiviral treatment).
immune population acting like not immune
The process of an organism stopping to experience any symptoms caused by a disease.
becoming asymptomatic
The process of an organism beginning to experience symptoms caused by a disease.
becoming symptomatic
The process of an organism beginning to experience severe symptoms caused by a disease.
becoming severely symptomatic
A process profile that specifies the degree to which a host is likely to pass on an infection to a susceptible organism.
This is probably a 'process profile' according to BFO2
infectiousness profile
The disposition of one or more portions of material entity, when administered to a susceptible organism by a certain route and according to a certain schedule, to produce a structural change in an organism of a specific species, whereby this structural change serves as the physical basis of a protective resistance disposition.
infectious disease treatment efficacy
A travel-related infectious disease control strategy that has an action specification that is realized in restricting movement of organisms across international borders.
border control strategy
an infectious disease control strategy that has an action specification that is realized in closing facilities where organisms congregate during times when the facilities normally would be open.
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.
place closure control strategy
an infectious disease control strategy that has an action specification that is realized in isolating organsims who are infectious.
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.
case isolation control strategy
A travel-related infectious disease control strategy whose action specification is realized in restricting travel of organims from one ecosystem to another ecosystem
A travel-related infectious disease control strategy whose action specification is realized in restricting travel of organims from one geographical region to another
travel restriction control strategy
A taxonomy identifier that denotes a group of organisms or groups of organisms based on common ancestors.
A reference to a group or groups of organisms that are based on common ancestry.
Some regard a clade to be a single branch on the tree of life. [http://en.wikipedia.org/wiki/Clade]
clade name
A population of only infected members of one species.
infected population
A population of organisms that are all susceptible.
susceptible population
A population of organisms that are all immune.
immune population
asymptomatic host
An organism of a particular biological taxon that is the bearer of an infectious dispositions towards an organism of a different particular biological taxon.
An organism, virus, or prion that can infect another organism.
pathogen
An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon.
host
A disease that inheres in a host and, when realized, is realized as a disease course that is causally preceded by an infection.
A disease that is caused by an infection.
Infection is the etiological process, as defined by OGMS, for infectious disease. However, OGMS does not relate its etiological process class to its disorder class as of this writing. So it is not clear how to connect infectious disease to its infection etiological process.
infectious disease
A information content entity that specifies the date of a census.
census reference date
An information content entity specifying the upper and lower limit of a range of ages of continuants.
age range category
A name of temporal region that specifies a time span on a specified time scale by giving a start time and a duration.
An information content entity that specifies a time span on a specified time scale by giving a start time and a duration.
name of temporal interval
A measurement datum that quantifies a temporal region that is occupied by a processual entity.
duration
a unique identifier that refers to a disease.
A unique identifier that refers to a particular type of disease.
This class is different from its superclass, in that the identifier is non-redundant with other identifiers in its context (such as a coding system or terminology or ontology). The superclass admits of natural langugage names of diseases, whereas this one typically does not.
We still need to decide which coding schema to adopt.-MB
disease unique identifier
A probability distribution of two jointly distributed random variables X and Y, where Y is know to be a particular value.
conditional probability distribution
In the study of probability, given at least two random variables X, Y, ..., that are defined on a probability space, the joint probability distribution for X, Y, ... is a probability distribution that gives the probability that each of X, Y, ... falls in any particular range or discrete set of values specified for that variable.
joint probability distribution
An unconditional probability distribution is the probability distribution of an uncertain variable, U, implicitly incorporating the uncertainty introduced by any other relevant variables. Mathematically, U’s unconditional probability distribution is written {U | E}, where E represents the background state of information under which the distribution is assessed.
unconditional probability distribution
obsolete parametric probability distribution
nonparametric probability distribution
discrete parametric probability distribution
continuous parametric probability distribution
discrete nonparametric probability distribution
continuous nonparametric probability distribution
A continuous parametric probability distribution that takes as its input a normally-distributed logarithmic function with mean μ and standard deviation σ.
a log-normal (or lognormal) distribution is a continuous probability distribution of a random variable whose logarithm is normally distributed.
log normal distribution
the gamma distribution is a two-parameter family of continuous probability distributions
gamma distribution
A continuous parametric probability distribution that gives the distribution of lifetimes of objects. It was originally proposed to quantify fatigue data, but it is also used in analysis of systems involving a "weakest link."
Weibull Distribution
the continuous uniform distribution or rectangular distribution is a family of symmetric probability distributions such that for each member of the family, all intervals of the same length on the distribution's support are equally probable.
continuous uniform distribution
The duration between the appearance of symptoms of a disease and the start of a treatment.
delayFromSymptomsToTreatment
delay from symptoms to treatment
An identifier that refers to a particular geographical region and that is constructed per guidelines of the Apollo project.
A hierarchical identifier beginning with an ISO 2-letter nation code (e.g., US) and that represents one partition of an exclusive and exhaustive partitioning of that nation (including the trivial case of just representing the entire region of the nation).
apollo location code
An information content entity that specifies the time at which an infectious disease control strategy ends.
control strategy stop time information
A rule that specifies the event that, when it occurs, is the trigger to either start or stop an infectious disease control strategy.
A rule that says when to start or stop a control strategy. It can be either the passage of time, a disease surveillance result (exceeding the threshold of a certain fraction of the population that is infected), or a treatment surveillance result (reaching a certain fraction of the population that has received an antiviral or vaccination).
infectious disease control strategy trigger definition
The probability of the occurence of a contamination acquisition from either an infected organism or another contaminated thing.
contamination probability
A measurement datum of the time interval from the decision to cease an infectious disease control strategy to the time the control strategy ends expressed in number of time intervals.
A period from the conclusion of a control strategy until its disease-controlling activities actually end. For example, it may take time to communicate to workers to stop vaccinating and thus they keep vaccinating for some time after the control strategy is concluded.
control strategy stand-down delay
An infection acquisition whereby a susceptible host acquires an infection from a contaminated thing.
An infection acquisition from a contaminated thing.
infection acquisition from contaminated thing
An infection acquisition whereby a susceptible host acquires an infection from an infectious host.
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.
infection acquisition from infectious host
A disposition of a disease surveillance infrastructure to detect the outbreak of one particular disease in the geographical region the infrastructure aims to cover.
A capability associated with a location to detect individuals in a population with a particular type of disease.
Specifies location, pathogen, host taxon, caseDefinition, sensitivity, specificity, and time delay of case detection
disease surveillance capability
The duration from the time an organism satisfies a case definition until a process or system detects the organism as satisfying that case definition
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 delay to case detection
An identifier that designates a scale according to which time is measured (e.g., Gregorian Calendar).
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.
time scale name
An infectious disease control trigger definition for a reactive control measure based on the outcome of disease surveillance.
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.
disease surveillance trigger definition
treatment surveillance trigger definition
An infectious disease control trigger definition that is based on the passage of a specified interval of time.
A control strategy trigger that occurs once a constant duration of time has elapsed.
temporal trigger definition
the duration of time that has elapsed from the zero reference point to a later time on the time scale
A duration of time that has elapsed since the zero reference point of a time scale.
time since time scale zero
seasonal function parameter
maximum seasonal latitude
minimum seasonal latitude
seasonal temporal offset
The sensitivity of a system that classifies organisms into the binary categories of individual who meets the criteria of a particular case definition and individual who does NOT meet the criteria of a particular type of disease X.
The sensitivity of a process or system that detects organisms who satisfy a case definition.
sensitivity of case detection
The probability that entry is denied as part of a border control strategy.
probability of entry into a country is denied
The probability that exit is denied as part of a border control strategy.
probability of exit from a country is denied
A duration that measures the temporal interval occupied by a treatment course.
A period from the start to the end of a treatment course.
duration of treatment course
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
number of doses in a treatment course
A specification of the target populations of a control strategy and the priority of each population in the strategy.
target populations and prioritizations information
An epidemic simulator action specification that specifies the factor by which to multiply the transmission coefficient for contacts that occur in a school.
A factor by which to multiply the transmission coefficient for contacts that occur in in a school.
school transmission multiplier
An epidemic simulator action specification that specifies the factor by which to multiply the transmission coefficient for contacts that occur in a household.
A factor by which to multiply the transmission coefficient for contacts that occur in a household.
household transmission multiplier
An epidemic simulator action specification that specifies the factor by which to multiply the transmission coefficient for contacts that occur in a workplace.
A factor by which to multiply the transmission coefficient for contacts that occur in a workplace.
workplace transmission multiplier
A place-closure control strategy that decides on a case-by-case basis whether to close places of a certain type, as opposed to blanket policy that closes all places of a certain type at the same time.
close individual places independently strategy
The duration from the closure of a place until the time when it is reopened.
place closure period
community transmission multiplier
maximum travel distance in km information
An objective specification that specifies the disease outcome that a treatment seeks to prevent.
William Hogan
treatment preventable outcome
The duration from the time an individual receives a treatment until the time a system designed to detect that the treatment occurred detects it in a population
The duration from treatment until a treatment surveillance system detects it in a population
time delay of treatment detection
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'.
individual treatment strategy supply schedule unit of measure
The unit of measure for the administration capacity of an individual treatment. For example, 'daily dose'.
administrationCapacityUnits
individual treatment strategy administration capacity unit of measure
A disease transmission model that explicitly represents each individual in the population and simulates the acquisition of disease by individuals who do not already have it at simulator time zero.
agent-based disease transmission model
A unit of measure for a threshold in a reactive infectious disease control strategy.
reactive control strategy threshold unit of measure
An information content entity that specifies the criteria that an organism must meet to be considered to be in some abnormal state.
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.
case definition
A period during which an infectious host organism is isolated from contact with other organisms in the ecosystem as part of a quarantine control strategy.
obsolete quarantine period
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.
epidemic of infection
A process whose beginning is demarcated by accelerating infection acquisition by one or more host species of a particular pathogen in a particular location and whose end is demarcated by the time when the rate of of infection acquisition becomes constant. The constant rate may be zero. The period of an epidemic may be defined using statistical criteria based on incidence rates or causal models based on their fit to incidence data.
An example of multiple host species is foot and mouth disease (such as the 2001 epidemic in the UK, see: http://www.sciencemag.org/content/292/5519/1155.long) and swine flu. The foot and mouth disease epidemic affected sheep, pigs, and cattle.
epidemic
An immune organism that acts as if it is immune (i.e., it does not seek vaccination or avoid contact with infectious organisms).
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.)
immune organism that acts like it is immune
An immune organism that acts as if it is NOT immune (i.e., it seeks vaccination and/or avoids contact with infectious organisms).
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.)
immune organism that acts like it is not immune
An immune resistance to infection that is causally preceded by an infection and an immune response to that infection with the production of antibodies to antigens from the pathogen population participating in the infection.
naturally-acquired active immune resistance
An organism that is the bearer of a naturally-acquired, active immune resistance to infection.
An organism that has recovered from infection with a particular pathogen, is no longer infectious to other organisms of any species, and is not able to be infected again with that pathogen.
recovered
recovered organism
A disease transmission model that represents populations of susceptible and infected individuals (but not these individuals directly themselves) and simulates movement of individuals from one such population (a.k.a. compartment) to another.
compartmental disease transmission model
An individual treatment control strategy that has as part an action specification that is realized in anti-infective treatment.
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.
anti-infective individual treatment control strategy
An anti-infective individual treatment control strategy that has as part an action specification that is realized in antibacterial treatment.
An anti-infective individual treatment control strategy that uses anti-bacterial medications to treat infected hosts in an attempt to limit their infectiousness and/or infectious period.
anti-bacterial control strategy
infection in an ecosystem
A process comprised of numerous infections and infection acquisitions with a particular pathogen in one or more populations of hosts.
A process of ongoing infection and infection acquisition in individuals in one or more populations in an ecosystem.
infection in ecosystem
endemic
An infectious disease control strategy that has a vector control action specification as part.
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'.
Typically, the strategy is to limit the population of the second host species, which is called the "vector" for the infection.
vector control strategy
A census of entities of a certain type or types in the abiotic ecosystem.
A census of things in the abiotic ecosystem.
abiotic ecosystem census
An action specification that is realized in reducing the number of infection acquistions in one population of a particular species from infectious hosts in a population of another particular species, called the "vector".
vector control action specification
The average number of water containers testing positive for the presence of a particular mosquito species, typically Aedes aegyptii, per 100 households in the geographical region under surveillance.
The average number of containers positive (for presence of mosquito) per 100 households.
Breteau Index
A multicellular organism reproduction that has as its agent a mosquito (taxon Culicidae, ID 7157)
Reproduction of a single mosquito
individual mosquito reproduction
The duration of the temporal interval occupied by a gonotropic period.
The duration of the gonotrophic cycle in a female mosquito.
gonotrophic cycle duration
The process in a female mosquito of taking a blood meal, developing eggs, and laying the eggs (oviposition).
gonotrophic cycle
An abiotic ecosystem census of the locations where pregnant female mosquitos lay their eggs.
A census of sites where mosquitoes have laid their eggs.
OvipositionSiteCensus
oviposition site census
The maximum number of ovisites in/around a single house or other dwelling structure.
obsolete carrying capacity per house
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.
incubation period
A treatment with a drug product.
Treatment with a drug.
drug treatment
An infectious disease control strategy whereby the household members of infectious indivduals voluntarily stay at home to avoid further potentially infectious contacts.
voluntary household quarantine control strategy
An infectious disease conrol straegy that seeks to reduce disease transmission by offering employees extra paid time off to stay home, in an attempt to reduce contacts that transmit disease in the workplace.
liberal sick leave control strategy
epidemic investigation study design
A study design that specifies which epidemic(s) to investigate, how, and what information to output.
epidemic investigation 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.
A vector control strategy that has an action specification that is realized by reducing the number of larval-stage organisms of a vector population.
A vector control strategy that kills larval-stage vector organisms
larvicide control strategy
biological colonization
a reproduction of a pathogen of a particular biological taxon inside a host organism of another taxon, without invasion of the tissues of the host.
Primary use case is colonization of humans, animals with Staph aureus, but it also covers bacteriuria, transient bactermia, and normal gut flora.
colonization
infection in a population
an infection in an ecosystem occurring in one population of organisms
Infection
infection in population
colonization acquisition
a biological process where a pathogen organism of a particular biological taxon enters into a host organism of a particular taxon and begins to undergo reproduction in a location external to tissues of the host
the host organism was not colonized wtih the pathogen prior to the colonization acquisition
decolonization control strategy
an indivdiual treatment control strategy that prevents infectious disease by treating indivdiuals colonized with a pathogen of a particular species to limit or end the colonization
typically the pathogen is a bacterium
establishment of infection from self colonization
An infection acquisition by which a pathogen organism from a particular biological taxon, which previously was participating in a colonization process in a host organism from another taxon, begins to invade the tissues of the same host organism and reproduce there.
infection acquistion from self colonization
chemical resistance to infection
A resistance to infection that is conferred by the presence, in sufficient quantity, of a particular molecular entity that is not normally present in the organism.
chemoprotection
chemoprotective resistance
chemotherapeutic resistance to infection
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
resistance to malaria infection
A resistance to infection by P. vivax, P. ovale, P. malariae, and/or P. falciparum.
malaria resistance
resistance to malaria
A symbiosis where the organisms that are interacting remain physically external to one another.
It includes situations where one organism lives on the surface of the other organism.
ectosymbiosis
An ectosymbiosis that results in harm to all participating organisms.
Example: competition between lions and hyenas for food
antagonism
An ectosymbiosis that results in harm to one of the participating organisms but neither harms nor benefits the other participating organisms.
Example: Spanish ibex and weevils of the genus Timarcha
amensalism
An ectosymbiosis that results in harm to one of the participating organisms and benefit to another participating organism.
agonism
An agonism where the participating organisms, although physically external to one another, nevertheless have close and persistent physical contact for most or all of the interaction.
intimate agonism
An intimate agonism in which the harm is not fatal to the host.
ectoparasitism
Example: Temnocephala chilensis and various marine wildlife
ectosymbiotic parasitism
An ectosymbiotic parasitism that realizes some facultative parasite role inhering in an organism that is also realized by a bodily benefit to that organism.
facultative ectoparasitism
An ectosymbiotic parasitism that realizes a disposition of the parasite that is not one of its biological functions.
Example: Armillaria (type of wood fungus) and trees
facultative ectosymbiotic parasitism
An ectosymbiotic parasitism that realizes a biological function that inheres in some proper part of the parasite.
obligatory ectoparasitism
Example: European common cuckoo and other bird species (brood parasitism)
obligatory ectosymbiotic parasitism
An intimate agonism in which the harm is fatal to the host.
ectoparasitoidism
ectosymbiotic parasitoidism
An ectosymbiotic parasitoidism that realizes some facultative parasitoid role inhering in an organism that is also realized by a bodily benefit to that organism.
facultative ectoparasitoidism
An ectosymbiotic parasitoidism that realizes a disposition of the parasitoid that is not one of its biological functions.
Example: Pachycrepoideus dubius and Ceratitis capitata
facultative ectosymbiotic parasitoidism
An ectosymbiotic parasitoidism that realizes a biological function that inheres in some proper part of the parasitoid.
obligatory ectoparasitoidism
Example: Mutillidae (family of wasps) and other wasps/ants
obligatory ectosymbiotic parasitoidism
An ectosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms.
ectocommensalism
ectosymbiotic commensalism
An ectosymbiotic commensalism that realizes some facultative commensal role inhering in an organism that is also realized by a bodily benefit to that organism.
facultative ectocommensalism
An ectosymbiotic commensalism that realizes a dispostion of the organism that benefits that is not one of its biological functions.
Example: Ophiodromus pugettensis and Patiria miniata
facultative ectosymbiotic commensalism
An ectosymbiotic commensalism that realizes a biological function that inheres in some proper part of the commensal organism that benefits.
obligatory ectocommensalism
Example: Basicladia algae and sea turtles
obligatory ectosymbiotic commensalism
An ectosymbiosis that results in benefit to all participating organisms.
ectomutualism
ectosymbiotic mutualism
An ectosymbiotic mutualism that realizes some facultative mutualist role inhering in an organism that is also realized by a bodily benefit to that organism.
facultative ectomutualism
An ectosymbiotic mutualism that realizes one or more dispositions of one or both organisms and these dispostions are not biological functions of either organism.
Example: ants that feed off of honeydew from aphids, and in turn protect the aphids
facultative ectosymbiotic mutualism
An ectosymbiotic mutualism that realizes a biological function that inheres in some proper part of at least one of the organisms participating.
obligatory ectomutualism
Example: bees and flowers
obligatory ectosymbiotic mutualism
A symbiosis where one organism is physically contained within another organism (called the 'host').
endosymbiosis
An endosymbiosis that results in benefit to the parasite and harm to the host.
endoparasitism
endosymbiotic parasitism
An agonism where the participating organisms maintain significant physical separation from one another through most or all of the interaction.
transient agonism
A non-intimate agonism in which the harm is fatal.
Example: lion and gazel
predation
A non-intimate agonism in which the harm is not fatal.
Example: Giant panda and bamboo
grazing
An endosymbiotic parasitism that realizes some facultative parasite role inhering in an organism that is also realized by a bodily benefit to that organism.
facultative endoparasitism
An endosymbiotic parasitism that realizes a disposition of the parasite that is not one of its biological functions.
Example: Strongyloides stercoralis (roundworm) and humans
facultative endosymbiotic parasitism
An endosymbiotic parasitism that realizes a biological function that inheres in some proper part of the parasite.
obligatory endoparasitism
Example: Necator americanus (hookworm) and humans
obligatory endosymbiotic parasitism
An endosymbiosis that results in benefit to the parasitoid and is fatal to the host.
endoparasitoidism
endosymbiotic parasitoidism
An endosymbiotic parasitoidism that realizes some facultative parasitoid role inhering in an organism that is also realized by a bodily benefit to that organism.
facultative endoparasitoidism
An endosymbiotic parasitoidism that realizes a disposition of the parasitoid that is not one of its biological functions.
Example: Naegleria fowleri (brain-eating amoeba) and humans
facultative endosymbiotic parasitoidism
An endosymbiotic parasitoidism that realizes a biological function that inheres in some proper part of the parasitoid.
obligatory endoparasitoidism
Example: Ichneumon eumerus (wasp) and Phengaris rebeli (butterfly caterpillar)
obligatory endosymbiotic parasitoidism
An endosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms.
endocommensalism
endosymbiotic commensalism
An endosymbiotic commensalism that realizes some facultative commensal role inhering in an organism that is also realized by a bodily benefit to that organism.
facultative endocommensalism
An endosymbiotic commensalism that realizes a dispostion of the non-host organism that benefits that is not one of its biological functions.
Example: Malaria and mosquito vector
facultative endosymbiotic commensalism
An endosymbiotic commensalism that realizes a biological function that inheres in some proper part of the commensal organism that benefits.
obligatory endocommensalism
Example: Passalurus ambiguus (nematode) and rabbits
obligatory endosymbiotic commensalism
An endosymbiosis that results in benefit to all participating organisms.
endomutualism
endosymbiotic mutualism
An endosymbiotic mutualism that realizes some facultative mutualist role inhering in an organism that is also realized by a bodily benefit to that organism.
facultative endomutualism
An endosymbiotic mutualism that realizes one or more dispositions of one or both organisms and these dispostions are not biological functions of either organism.
Example: Hamiltonella defensa and aphids
facultative endosymbiotic mutualism
An endosymbiotic mutualism that realizes a biological function that inheres in some proper part of at least one of the organisms participating.
obligatory endomutualism
Example: marine worms of genus Riftia and their endosymbiotic bacteria
obligatory endosymbiotic mutualism
A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning.
deprecated homeostasis
A process that has as output a material entity that is the material basis for an abnormal homeostasis dispostion.
bodily harm
A process that facilitates the realization of one or more normal homeostasis dispositions borne by an organism and/or one or more causally relatively isolated parts of the organism.
bodily benefit
An organism participating in an ectosymbiotic or endosymbiotic parasitism as the organism that benefits.
parasite
An organism participating in an ectosymbiotic or endosymbiotic parasitoidism as the organism that benefits.
parasitoid
An information content entity that is part of an infectious disease control strategy and that specifies the intended population to which one or more interventions in the control strategy will be applied.
target population definition
A name of temporal region that designates a temporal boundary
An information content entity that designates a temporal boundary
name of a temporal boundary
An information content entity that specifies a geographical region by (1) listing the names of other geographical regions whose mereological sum constitutes it and optionally (2) listing the names of other geographical regions that are subsequently subtracted from the mereological sum.
location definition
A contraindication that increases the risk of a treatment.
treatment contraindication
A duration that is specified as a probability distribution over a range of numbers.
uncertain duration
A measurement datum that is the fraction of things of a particular type in a particular geographical region or site that are contaminated with a pathogen.
fraction of contaminated thing
specificity of case detection
The specificity of a system that classifies organisms into the binary categories of individual who meets the criteria of a particular case definition and individual who does NOT meet the criteria of a particular type of disease X.
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 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.
specificity of treatment detection
The sensitivity of a system that classifies organisms into the binary categories of having received a particular treatment and not having received a particular treatment.
The sensitivity of the process or system that detects organisms that have undergone a particular treatment.
sensitivity of treatment detection
A duration that is specified as a single number.
fixed duration
real time span category definition
real date span category definition
An objective specification to observe all the organisms of a particular taxon in a particular geographical region or place and create a data set about them.
census objective specification
A plan specification with a census objective specification.
census plan specification
A planned process that realizes a census plan specification.
census taking
A vector control strategy that is realized by releasing individuals of the vector population infected with bacteria of the taxon Wolbachia to inhibit reproduction of individuals in the vector population.
Wolbachia vector control strategy
A vector control strategy that is realized by spraying chemicals in a place to kill individuals of the vector population.
indoor residual spraying vector control strategy
A vector control strategy for mosquitoes that is realized by reducing the number of water-containing vessels in which mosquitoes can lay eggs.
container reduction vector control strategy
An information content entity that specifies how many doses or courses of treatment, per a particular unit of time (typically one day), can be supplied for a given geographical region and/or how many of those doses or courses can subsequently be administered.
treatment system logistics
A disposition of a treatment surveillance infrastructure to detect individuals who have received treatment in the geographical region the infrastructure aims to cover.
treatment surveillance capability
name of temporal region
A population survey that assesses the presence (plus or minus quantity) of antibody to a particular antigen in individuals in a population.
population serology survey
A data set that is a collection of case records.
infection case list
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.
infection case record
A count of individuals in a population who meet an infection case definition during a particular time interval.
deprecated infection case count
The temporal interval occupied by an epidemic.
epidemic period
epidemic interval
An individual behavior of a mosquito (organism of family Culicidae).
individual mosquito behavior
An individual behavior of a human being.
individual human behavior
A data structure that represents, for a particular infection in ecosystem, a subset of infected organisms and for each infected organism in the subset except the first one infected temporally, its infection acquisition from an infected host as a machine-readable link to that infected host.
Because a set A is a subset of itself, we capture the possibility that all infected organisms in the epidemic are represented in the tree.
This definition allows for multiple trees in an epidemic because we did not require that the first case infected temporally be the index case, although the ideal situation is that there is one tree for the epidemic that includes the index case.
transmission tree
infectious disposition
A disposition inhering in an organism of a particular biological taxon that is realized only by the organism participating in an infection as the reproducing organism inside another organism of a different particular biological taxon.
The disposition of Influenza A virus H3N2 subtype to infect human beings, the disposition of Plasmodium vivax to infect mosquitos and humans, the disposition of foot and mouth disease virus to infect cloven-hooved animals (sheep, cows, pigs, etc.).
infectiousness
potentially infectious contact process
A biological process that brings the organism into sufficiently close physical proximity to a pathogen population, either in or on a contaminated thing or an infectious host, such that the organism is likely but not certain to acquire an infection with the pathogen.
potentially infectious contact
potentially infectious contacting
potentially infectous contact role
A role borne by an organism that is realized in a potentially infectious contact process.
contact role
infectious contact role
The organism bearing this role is the organism at risk for acquiring an infection when the role is realized. Also, this role differentiates participants in a process when there are two organisms participating, so it only begins to exist during its realization, justifying its existential restriction.
potentially infectious contact role
potentially infectious contact organism
An organism that is the bearer of a potentially infectious contact role during a potentially infectious contact process.
An organism that has been exposed to a pathogen by coming into close physical proximity with either an infectious host or a contaminated thing.
contacted organism
potentially infectious contact definition
An information content entity that specifies which kinds of processes involving an interaction between a given organism and either (1) another, potentially infectious organism or (2) a contaminated environment have a sufficiently high probability of resultling in an infection acquisition by the organism to be of interest to an outbreak investigation.
contact definition
An individual treatment control strategy that immediately targets individuals in the population who are at the perimeter of an epidemic.
ring individual treatment control strategy
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.
Wolbachia release site
A vector release site action specification for a Wolbachia control measure.
A vector control action specification that specifies the location of Wolbachia release sites according to some predetermined spatial interval.
Wolbachia every nth site release action specification
The rate at which offspring of the Wolbachia-infected female mosquito subpopulation (of the overall mosquito population) are not infected with Wolbachia.
leakage rate of Wolbachia infection in mosquito population infected with Wolbachia
The rate at which bites of mosquitoes infected with both Wolbachia and a particular pathogen such as dengue result in an infection in a susceptible human host.
transmission rate of pathogen to human from Wolbachia-infected mosquito bites
A vector control strategy that is realized by reducing the number of adults in a vector population.
adult vector control strategy
An adult vector control strategy that is used prior to a Wolbachia vector control strategy to increase the percentage of the adult population that gets infected with Wolbachia.
Wolbachia prerelease adult vector control strategy
An larvicide vector control strategy that is used prior to a Wolbachia vector control strategy to increase the percentage of the population that gets infected with Wolbachia.
Wolbachia prerelease larvicide vector control strategy
A data structure that refers to (1) a subpopulation of a population based on life stage, (2) the rate of mortality of that subpopulation, and (3) the average duration of time that the individuals in the subpopulation spend in that life stage.
life stages with duration and mortality
A process of change in the egg mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population.
Wolbachia effect on egg mortality rate in mosquito population
A process of change in the adult mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population.
Wolbachia effect on adult mortality rate in mosquito population
A process of change in the larval mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population.
Wolbachia effect on larval mortality rate in mosquito population
A process of change in fecundity of females in a mosquito population that is the outcome of an infection in that population with a Wolbachia bacteria population.
Wolbachia effect on female fecundity in mosquito population
A data item that specifies both an interval estimate centered around some sample statistic, and the probability that the process/method of obtaining the interval estimate's range of values will generate an interval that contains some unobserved population parameter of interest.
confidence interval
A seed release interval for a Wolbachia control measure.
Wolbachia release interval
A data structure that specifies both the sample mean and the confidence interval generated by the measurement process.
mean with confidence interval
A data structure that specifies both the sample mean and the standard deviation generated by the measurement process.
mean with standard deviation
A vector control action specification that specifies the number of Wolbachia-infected adult mosquitoes to be released at each household for some Wolbachia control measure.
A vector control action specification that specifies the number of Wolbachia-infected adult mosquitoes to be released at each household.
number of Wolbachia-infected mosquitoes released per house
An epidemic simulator action specification that when set to true, results in the simuator clearing each simulated Wolbachia-infected mosquito of its simulated Wolbachia infection whenever it migrates out of the simulated population location.
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.
clear Wolbachia upon vector migration
A predicted data item expressing the probability that a disease outcome occurs during the disease course of an organism.
disease outcome with probability
A name of a temporal region that is systematized according to a particular calendar system, such as the Gregorian calendar.
date
A scalar value specification that gives the diameter in meters of the circular area around which all organisms in a population are living will receive a vaccination as part of a ring vaccination control measure.
ring diameter in meters
An epidemic simulator actions specification that specifies the factor by which to multiply the mating probability of a male mosquito if it is infected with a Wolbachia bacterium.
Wolbachia effect on mating probability
A data item that specifies the smallest numerical value in a data set of scalar measurement data items.
minimum value
A data item that specifies the largest numerical value in a data set of scalar measurement data itmes.
maximum value
A predicted data item that estimates how reliable some method of statistical inference will be at estimating the population parameter of interest.
statistical confidence
A one-dimensional temporal region occupied by a place closure control strategy.
closure period
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.
lower bound
A measurement datum that is the fraction of a particular adult vector population that have undergone 1) infection acquisition with a pathogen, and 2) have experienced some outcome of the resulting infection.
fraction of vector adults affected
A measurement datum that is the fraction of eggs laid by a particular host population that has been destroyed and thus will not develop into a new member of the population.
fraction reduction of eggs
A measurement datum that is the fraction of the larval subpopulation of a particular host population that has died due to some event in the population (e.g, due to a particular control measure).
fraction reduction of larvae
A length measurement datum that specifies the radius of a circle, which is centered at a vector organism, for which there is a certain probability that the vector organism will bite a susceptible host.
vector bite radius
A duration that measures the temporal interval between some vector bite n and some vector bite n+1.
time between vector bites
A rate measurement datum of that divides the total distance traveled during some migration process by the duration of the temporal interval occupied by that process.
migration speed
An information content entity that specifies the probability that a given mosquito will realize a disposition to seek out a shaded environment when it isn't seeking a host or ovisite.
shade affinity
A rate measurement datum that specifies the ratio of distance travelled during a movement process to the duration of the time interval occupied by the process.
movement speed
A rate measurement datum that specifies the percentage of organisms within a population that have died over a given time interval.
mortality rate
A data item that specifies, as a ratio, the total count of oviposition sites located externally to all places in a geographic region relative to the total count of oviposition sites located internally to some place in that geographic region.
ratio of outdoor to indoor ovisites
An information content entity that delimits an interval data structure based on some value that is greater than or equal to all other values within that data structure.
upper bound
A data item that specifies the dispersion of values around some parameter in a set of data, and whose values are standardized to express the same unit of measure as the parameter of interest.
The duration of some process wherein one or more potentially infectious contact organisms (i.e., contacted organisms) are under physical isolation from other organisms within a population.
quarantine period
The probability that some male mosquito and some female mosquito within a certain distance of each other realize some disposition to reproduce with one another.
mosquito mating probability
An information content entity that specifies the probability that a given mosquito realizes some disposition to seek out a building if it isn't seeking a host or ovisite.
affinity for buildings
An epidemic simulator action specification that specifies the linear distance a female mosquito will travel to find the next oviposition site after depositing some of its eggs at the previous one.
linear distance travelled between oviposits
An average value that specifies the number of eggs produced during one reproductive cycle for each individual female within a population.
eggs per brood
A disposition of an organism to (i) undergo some bodily benefit that (ii) is triggered by a planned process.
We often say in natural language it is the efficacy of the triggering planned process such as vaccination. However, processes do not have properties such as roles, dispositions, functions, qualities in BFO. And this is also not a process profile, because it is not the process of a quality changing values (determinates) over time. Nevertheless, it is natural to classify efficacies based on the type of triggering process because that is what differentiates what happens when they are realized. For example, a vaccination efficacy will be realized through different processes than a quarantine efficacy. For individual treatments, the triggering process is a treatment (as defined by OGMS).
efficacy
A temporal part of a disease course that itself has a temporal part of becoming symptomatic, followed by another temporal part that is characterized by the organism experiencing mild, non-disease-specific symptoms.
prodromal period
A temporal part of a disease course that 1) itself has a temporal part of becoming severely symptomatic, 2) terminates in either death or some bodily harm, and 3) has a sudden onset and short duration.
Although it is often or even typically preceded by a prodromal period, it is not always the case. Therefore "immediately preceded by some prodromal period" cannot be a necessary condition.
fulminant period
The probablity that a female mosquito feeds on or probes the host given an interaction between the mosquito and the host that brings them within a certain proximity (the bite radius).
The probability that a female mosquito feeds on or probes the host given an interaction between the mosquito and the host that brings them within a certain proximity (the bite radius).
vector bite probability
A length measurement datum that specifies the radius of a circle, which is centered at a male vector organism, for which there is some probability that it will mate with a female mosquito.
male mosquito mating radius
A length measurement datum that specifies the radius of a circle that defines the geographical region in which some infectious disease control strategy will be implemented.
infectious disease control strategy cover radius
A taxonomy identifier curated by the NCBI taxonomy database that specifies the taxonomic classification of some organism that is the recipient of some treatment.
An identifier curated by the NCBI taxonomy database that specifies the taxonomic classification of some organism that is the recipient of some treatment.
species of treated organism
An identifier that denotes a drug product.
drug identifier
A data structure that holds the mean, median, minimum value, and maximum value of one set of measurement data.
mean median minimum maximum summary statistics data structure
A conditional specification for some epidemic simulator that is triggered by a Boolean value that, if true, specifies that there is a non-uniform distribution of oviposition site carrying capacities in a simulated vector population.
heterogenous carrying capacity
A site that is the bearer of a role that is realized by the release of artificially-infected vectors for the purpose of infecting the local vector population with a certain pathogen.
seed site
A vector control action specification that is realized by releasing artificially-infected vector organisms at the specified time intervals.
seed release interval
A vector control action specification that specifies the location of vector release sites according to some predetermined spatial interval.
vector release site action specification
A vector control action specification that specifies the number of artificially-infected vectors to be released at each household.
number of artificially-infected vectors released per house
An epidemic simulator action specification that, when set to true, results in the simulator clearing each simulated artificially-infected vector of its simulated infection whenever it migrates out of the simulated population location.
clear infection upon vector migration
An identifier curated by IHTSDO that refers to some representational unit within its class hierarchy.
SNOMED concept identifier
A data item that is about a proposition and has a numeric value between 0 and 1, inclusive, that is the output of some process of inference, such that 1) logical falsehoods and logical truths are assigned a value of 0 and 1, respectively, while contingent propositions are assigned some intermediate value; and 2) the process of inference conforms with rules for the calculation of probabilities, and that any interpretation of probability must specify the extent to which probabilities might be used to constrain the degrees of belief of rational agents.
The first criterion is derived from Kolmogorov's Probability Calculus, while the second is derived from Salmon's Admissibility and Applicability Criteria of Adequacy. Salmon's ascertainability criterion is subsumed by the definition for 'data item'.
probability
An epidemic simulator action specification that specifies the minimum number of eggs that any simulated female mosquito will oviposit during a gonotrophic cycle.
minimum eggs per oviposition site
A rate measurement datum that measures the percentage decrease per unit time (typically per day) in the number of offspring to which a female mosquito passes an infection with a particular pathogen (e.g., Wolbachia).
age-dependent fecundity reduction
An epidemic simulator action specification that specifies the maximum number of larvae that can exist across all ovisites in a given house.
Mosquitos can sense eggs in ovisite so tend to lay in places not at max.
carrying capacity per house
An epidemic simulator action specification that specifies the comparison operation to use to determine whether some value, relative to a threshold, is one that should trigger the implementation of a control measure.
reactive control measure operator
A time measurement datum of the length of the temporal interval occupied by a gonotropic period.
gonotrophic period duration
A textual entity that specifies characteristics of some entity.
description
A probability distribution where the probability of each outcome is the range of a function (whose domain is the outcomes) that is calculated using one or more constant values (called parameters).
parametric probability distribution
A vector control strategy that has 1) an action specification that is realized in releasing artificially-infected vector organisms into a vector population, and 2) an objective specification of spreading this infection throughtout the vector population.
seed infections into vector population control measure
A predicted data item that is the maximum value of larvae that some ovisite is capable of sustaining.
ovisite carrying capacity
A behavior of one or more organisms that is characterized by the displacement from one geographic region to some target geographic region, and is the realization of either a biological function or (a concretization of) an objective specification.
geographical migration of organism
An action specification that delineates some minimum value or maximum value for some test statistic within a continuous probability distribution that is meant to serve as a lower bound or upper bound, respectively, for some population or sample of interest.
cut-off point specification
A duration that measures a temporal region occupied by a prodromal period.
prodromal period duration
A duration that measures a temporal region occupied by a fulminant period.
fulminant period duration
A taxonomy identifier curated by the NCBI taxonomy database that has been used to specify the species of some organism in which some disease has been realized.
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.
identifier of species of diseased organism
A taxonomy identifier curated by the NCBI taxonomy database that has been used to identify the species of some organism that meets a case definition.
An identifier curated by the NCBI taxonomy database that has been used to identify the species of some organism that meets a case definition.
identifier for species of case
infectious disease control strategy to prevent infection acquisition by individuals traveling from one ecosystem to another ecosystem
An infectious disease control strategy that has an objective specification of preventing infection acquisition by organisms traveling from one ecosystem to another ecosystem.
travel-related infectious disease control strategy
travel recommendation infectious disease control strategy
A travel-related infectious disease control strategy that has an action specification that is realized by making recommendations to travelers to either (1) avoid travel to an ecosystem with an ongoing infection such as an epidemic, (2) take precautions when traveling to such an ecosystem, (3) receive certain vaccinations prior to traveling to such an ecosystem, or (4) take certain medications when traveling to such an ecosystem
A travel-related infectious disease control strategy that recommends to travelers to either (1) avoid travel to a region with an ongoing infection such as an epidemic, (2) take precautions when traveling to such a region, (3) receive certain vaccinations prior to traveling to such a region, or (4) take certain medications when traveling to such a region
travel recommendation control strategy
A case isolation control measure that has an action specification that is realized in preventing one or more infectious organisms from having physical contact with other organisms.
contact isolation control measure
A duration that measures the temporal interval occupied by some colonization.
colonization duration
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.
identifier of species of population
An identifier curated by the National Library of Medicine as a unique string of integer numerals to be used as a standard way of denoting each concept in the RxNorm terminology.
RxNorm drug concept identifier
An identifier curated by the Regenstrief Institute to be used as a standard way of denoting each term in the LOINC database.
LOINC identifier
A LOINC identifier that refers to some clinical laboratory test conducted in a particular context..
laboratory test LOINC identifier
An identifier curated by the United States National Library of Medicine and National Institutes of Health that denotes some publication record in the MEDLINE database.
PubMed identifier
An identifier curated by ORCID, Inc. to denote some academic author.
ORCID
A count of individuals in a population who meet the criteria of some case definition during some time interval.
count of disease cases
A count of disease cases in an infected population that meet the case definition criteria within a particular epidemic interval.
count of cases in an epidemic
An adult vector control strategy that has 1) an action specification that is realized by the use of insecticide-treated nets within households, and 2) an objective specification that is realized by preventing potentially infectious contacting between some mosquito vector and some human host.
insecticide-treated net control measure
A plan specification that specifies 1) the quantity of which some material entity will be allocated to the eventual realization of some action specification, and 2) the temporal regions in which each action specification is to be realized.
schedule
A population census about the organisms specific to that population that were the host in some colonization acquisition.
population colonization census
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.
drug treatment efficacy
A data set that comprises exactly one latitude measurement datum and exactly one longitude measurement datum as its elements, and optiionally the geodetic datum used as the coordinate system for the measurements, and each of these measurements is about the same zero-dimensional geographical region.
latitude and longitude coordinate pair
A time measurement datum that refers to the temporal interval occupied by the life course of some organism and that takes 'years' as its measurement unit label.
age in years datum
A duration that measures a temporal region occupied by some contamination.
contamination period duration
A healthcare facility identifier that refers to some architectural structure that is the bearer of some healthcare function.
healthcare facility identifier
An identifier that refers to some disease transmission model model.
disease transmission model identifier
An identifier that denotes some architectural structure.
facility identifier
An identifier that denotes a biological taxonomic group.
taxonomy identifier
An identifier that denotes an organism included in some infection case count.
disease case identifier
An infection acquistion from infectious host that is causally downstream of some potentially infectious sexual contacting
Note that infections that are acquired in this manner do not fall within the class of sexually transmitted infections (STI's), ipso facto. This type of transmission can also occur with non-STI pathogens--such as meningitis and Zika.
infection acquisition through sexual activity with infectious host
A rate measurement datum that is the result of the measurement of the volume of water produced by some hydrological precipitation process at a particular geographical region divided by the number of temporal intervals of equal duration over which the precipitation occurred.
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.
mean rate of hydrological precipitation
An average value that takes, as input, some set of air temperature measurement data that were recorded over a particular duration of time.
mean air temperature
A sexual activity with at least one infectious host as participant where the infectious host(s) are infected with a pathogen that has a disposition to infect the tissues of the non-infected host that came into physical contact with the infectious host during the activity.
potentially infectious sexual contacting
host population
A population of organisms some of which were susceptible to infection with a particular pathogen at some point in their lives.
population of host organisms
An action specification that is part of an infectious disease control strategy that has at least one rule pertaining to some control measure.
prioritization scheme for control measure
A data transformation that takes as its input exactly one continuous variable as a value and assesses whether any statistically significant change to that variable will produce some change to the model's output.
one-way sensitivity analysis of a continuous variable
An identifier that is an integer numeral that denotes some citation.
citation identifier
A geographic region that contains a sampling process.
location of sampling process
An infection acquisition from infectious host by an embryo, fetus, or baby from its infectious mother while in utero, in egg at any point prior to hatching (even after laying), or during childbirth.
congenital infection acquisition
infection acquisition from mother-to-child transmission
infection acquisition from vertical transmission
software source code version control repository
A data set that comprises at least one set of source code files for software as well as provenance information about who contributed the set of files, and optionally multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc.
Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based
source code repository
process of compiling software
A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions.
It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.).
Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code.
compiling software
machine instructions compiled from software source code
A software that is the specified output of some compilation of software process
compiled software code
An algorithm that models some scale-free network.
scale-free network model
A graph of vertices in which, for some fraction of vertices, P(k), the number of connections, k, varies as a power of some parameter, γ. In other words, P(k) ~ k^(-γ), where 2 < γ < 3.
scale-free network
A data set that represents 1) one or more collections of organisms at some time and some geographical region; and optionally 2) the school facilities, workplace facilities, and health care facilities in that region.
The interactions between each organism as they move between these facilities may also be included in the data set.
synthetic ecosystem data set
A probability whose value is dependent upon the occurrence, known or presumed, of some process.
conditional probability
A conditional probability whose value is dependent upon the duration of some colonization or infection.
probability of infection over time
A data item that specifies the number of susceptible organisms necessary for an epidemic to occur within a population.
epidemic threshold
A geographical migration of an organism belonging to the species Homo sapiens.
human travel
Human travel that involves 1) movement from one geographical region to another through the air as a temporal proper part, and 2) the use of some processed material (e.g., airplane, hang glider) for propulsion that has some function of mechanical flight.
human air travel
A data item that is about one or more instances of human travel, and that specifies the geographical start location, geographical end location, and the geographical regions visited throughout the process.
human mobility data item
A copyright license that is about some software and contains one or more conditional specifications that specify the use and redistribution of the software.
software license
An identifier that refers to a specific software license.
complete software license identifier
An identifier that, as part of a complete software license identifier, refers to one specific version of the software license.
software license version identifier
An identifier that refers to all versions of a specific software license.
software license identifier
A unique resource locator that constitutes a reference to some software license.
software license URL
model of population dynamics software application
An simulation software application that when realized simulates changes in the size and life stage distribution of a population or populations of organisms of a particular biological taxon.
An algorithm that simulates changes in the size and life stage distribution of a population or populations of organisms of a particular biological taxon.
population dynamics model
disease surveillance objective specification
An objective specification whose endpoint is human awareness of the level of a particular disease in a particular population of a given biological taxon during some time interval.
population mortality data set
A data set that is about either some mortality rate or the death events themselves of some individuals of a given population of a particular biological taxon.
mortality data
pathogen evolution model software application
A simulation software application that simulates the evolution over time of a particular pathogen of a particular biological taxon.
Matthew Diller
Simulation software that simulates the evolution over time of a particular pathogen of a particular biological taxon.
pathogen evolution model
A planned process that is the realization of a disease surveillance objective specification.
disease surveillance
Individual human behavior that involves either 1) remaining in some susceptible population or some exposed population or 2) human movement away from or around an infectious population, in order to avoid being participant in some infection acquisition.
self-initiated travel avoidance behavior
A data item that is about one or more instances of social interaction between two or more individuals, and that specifies the temporal duration of interaction, spatial distance of individuals, geographical location of individuals, and the number of individuals participant in some social behavior(s).
social interaction data item
A compartmental disease transmission model that represents some infection in ecosystem in which there is only a susceptible population and an infectious population, such that individuals who aren't infectious are susceptible.
Susceptible-Infected-Susceptible model
A compartmental disease transmission model that represents some infection in ecosystem in which there are compartments for susceptible individuals, infectious individuals, and recovered individuals, such that recovered individuals are immune to future infection.
Susceptible-Infected-Resistant model
An infectious disease control strategy that identifies and treats contacted organisms in a host population.
contact tracing
A compartmental disease transmission model that represents some infection in ecosystem in which there are compartments for susceptible individuals, exposed individuals, infectious individuals, and immune inviduals, such that exposed individuals are infected but cannot transmit the pathogen.
Susceptible-Exposed-Infectious-Recovered model
A disease transmission model that is about two or more collections of organisms of a particular biological taxon in separate geographical locations and some geographical migration of organisms between them.
metapopulation disease transmission model
A Susceptible-Infected-Resistant model that represents exactly two infections in ecosystem by exactly two pathogens.
two-strain Susceptible-Infectious-Resistant model
A data set that is about some disease surveillance.
disease surveillance data
disease transmission tree estimator software application
A software application that implements an algorithm that has specified output some transmission tree.
An algorithm that has specified output some transmission tree.
disease transmission tree estimator
A function inhering in some device that is realized by some movement process in the atmosphere in which the device is participant in.
mechanical flight function
software application that forecasts disease transmission
A simulation software application that has as output one or more predicted count data items that are about a host population and that predict how many infections will occur at or will have occurred at some temporal region relative to when the data items are created.
disease forecasting software
infectious disease forecaster
infectious disease forecasting software application
An investigation that realizes the concretization of some disease state design and that has as an occurrent part some population survey that has specified input some case definition.
An investigation following a disease state study design that includes a population survey as part, where a case definition used in the population survey to ascertain disease state.
case series
A data set that is the output of a case series investigation.
case series data set
A data set about an instance of an epidemic.
epidemic data set
disease transmission model software application
disease transmission model software
data format converter software application
data format converter
phylogenetic tree constructor software application
A software application that implements an algorithm that has specified output a phylogenetic tree
phylogenetic tree constructor
data visualizer software application
A software application that implements an algorithm that has some data visualizer software objective specification as part.
data visualizer
computational modeling toolkit software application
computational modeling toolkit
data parsing process
A data transformation that has a dataset, encoded in a particular data format specification, as input and extracts certain elements or parts of the dataset, typically into the volatile memory of a computer.
data reading process
reading data
data parsing
synthetic ecosystem constructor software
A software that when compiled and run, has specified output of an agent-level ecosystem data set.
software for creating a synthetic ecosystem dataset
example: Synthia, SPEW
synthetic ecosystem constructor
A data item that is the output of some infection case count and that represents the number of infectious disease cases that ended in death.
total fatal disease cases
A count of the total number of diseased indivduals in a population during a particular time interval.
The total number of diseased individuals in a population at a point in time.
total disease cases
A data item that denotes some context in which an individual realizes some employee role if he or she is a member of the labor force, or the context in which he or she is not a member of the labor force according to certain prespecified conditions.
If an individual is a member of the labor force, the criteria that this status is selected from includes whether they are in the armed forces, employed and working, employed but absent from work for a week, and unemployed. The criteria for those not in the labor force includes whether the individual is a houseworker, suffering from a physical impairment that prevents them from working, in school, or other miscellaneous reasons.
employment status data item
An abiotic ecosystem element that is participant in some biological contamination process.
contaminated abiotic thing
An adult vector control strategy that has 1) an action specification that is realized by the use of mosquito traps that leverage natural or synthetic human odors as bait, and 2) an objective specification that is realized by preventing potentially infectious contacting between some mosquito vector and some human host.
odor-baited trap control strategy
An infectious disease control strategy that attempts to prevent infection of susceptible human host organisms in a particular geographical region by increasing the population of domesticated animals in that region, such that less mosquitoes feed on humans.
zoo-prophylaxis control strategy
A clinical phenotype that is causally preceded by some infection or some adverse drug reaction; and that is accompanied by a fever greater than or equal to 37.8 degrees Celsius, and a cough or sore throat.
influenza-like illness
acute respiratory illness
A scalar value specification whose measurement unit label is 'week' and that is part of the first predicted data item that is greater than the epidemic threshold set for that data item.
Amanda Hicks
epidemic start week
A scalar value specification whose measurement unit label is 'week', and that is part of the epidemic peak intensity.
epidemic peak week
A predicted data item that is about some aggregate of cases in an epidemic and whose value specification contains the maximum value in a data set that is about the epidemic.
epidemic peak intensity
A process that (1) has as occurrent parts at least two disease courses that realize the same type of disease, and (2) has as participants two or more hosts that are members of a particular host population.
aggregate of disease courses
A planned process that realizes some infectious disease forecasting software.
infectious disease forecast
An infectious disesae forecast that realizes some infectious disease nowcasting software.
infectious disease nowcast
An objective specification that is realized by the estimation of one or more predicted data items that are about 1) some infection in ecosystem and 2) potential changes to its number of participants (e.g., individuals within a host population, individuals within a vector population) relative to a particular temporal region; and is part of some infectious disease forecasting software.
infectious disease forecast objective specification
An infectious disease forecasting objective specification that is realized by the estimation of one or more predicted data items that are about some infection in ecosystem as they are occurring in real time, and is part of some infectious disease nowcasting software.
infectious disease nowcast objective specification
infectious disease nowcasting software application
An infectious disease forecasting software application that predicts how many infections are occurring within the same temporal interval that the data items are being estimated.
infectious disease nowcaster
An infectious disease forecast that has specified input some data set, the data items of which are about an infection in ecosystem that is current concomitant with the forecasting software’s executable code being realized.
prospective infectious disease forecast
An infectious disease nowcast that has specified input some data set, the data items of which are about an infection in ecosystem that is current concomitant with the forecasting software’s executable code being realized.
prospective infectious disease nowcast
An action specification that specifies the duration of time that is to elapse between each calculation of each predicted data item that is the output of some infectious disease forecast.
infectious disease forecast time specification
An inpatient encounter in which the health care provider role is realized by some person employed by the intensive care department of some health care facility, and the patient role is realized by someone admitted to that intensive care department.
intensive care unit encounter
An objective specification that is realized when a diagram is drawn from one or more data sets.
data visualization objective specification
treatment in the intensive care unit control strategy
an individual treatment control strategy that is realized by one or more intensive care unit encounters for infected individuals in the population
an individual treatment control strategy that is realized by treating one or more infected individuals in an intensive care unit
treatment in the ICU control strategy
website that has data as a part
This class was created for use case for MIDAS Digital Repository to index websites that have useful data in them, albeit rarely as machine-interpretable, downloadable datasets. Much of the data are locked in PDF or other text-based formats.
website with data
climate data set
A data set that is an aggregate of data items that are about an environmental system process (e.g., hydrological precipitation) or a participant in an environmental system process.
Matt Diller
metagenomics analysis software application
A software application that has as part an objective specification that is achieved by only a metagenomics analysis.
metagenomics analysis software
abiotic ecosystem data set
A data set that is about some abiotic ecosystem or abiotic ecosystem element.
abiotic ecosystem dataset
data set about an abiotic ecosystem or abiotic ecosystem element
A data set that is about an abiotic ecosystem or some abiotic ecosystem element.
atmospheric data set
A data set that is about either the Earth's atmosphere or some part of the Earth's atmosphere.
data set about Earth's atmosphere or some part of it
census of treatment facility
A census that counts the number of treatment facilities of some kind in a particular geographical region.
census of treatment facilities
treatment facilities census
treatment facility census
NOTE: this class counts the facilities themselves, not patients (people) in those facilities. For example, how many hospitals in a state. Not how many patients are in a hospital or hospitals in a state.
symbiosis
An interspecies interaction between two or more organisms in intimate association.
Martin BD, Schwab E. Current usage of symbiosis and associated terminology. International Journal of Biology. 2013 Jan 1;5(1):32. Available from: https://web.archive.org/web/20190723160720/https://www.researchgate.net/publication/233865641_Current_Usage_of_Symbiosis_and_Associated_Terminology
By "intimate interaction," we mean any interaction between two or more organisms that involves (1) physical contact or (2) multi-organism behavior in which all interacting organisms are participant.
data format validator software application
A software application that takes a data set as input and outputs a determination of whether the dataset is in compliance with one or more given data format specifications.
data format validator
disease identifier
an identifier that denotes a disease.
dataset about infectious disease acquisitions
The dataset at this link is rdf:type this class: https://figshare.com/articles/dataset/COVID19_settings_of_transmission_-_collected_reports_database/12173343
a dataset that is about infectious disease acquisitions at particular times and particular places.
The dataset may include sites (e.g. types of facilities, rooms), events (e.g., church service whether in or outdoors), dates, times, geographical regions, etc. in which the sites/events are located, and so on.
infection acquisition dataset
dataset about hospital stays
The datasets at this link are rdf:type this class: https://www.opendataphilly.org/dataset/covid-hospitalizations
a dataset that is about two or more hospital stays involving two or more patients.
hospital discharge dataset
hospitalization dataset
The dataset may be limited to stays in one hospital, but hospital discharge datasets as compiled by state departments of health typically contain stays from multiple hospitals (typically every hospital) in the geographical region over which they have jurisdiction
hospital stay dataset
human daily movement behavior
an individual human behavior that is the movements from one location to another throughout the day (e.g., work, home, stores, church, relatives' homes) in the areas adjacent to where the human lives at the time.
human daily movement
human daily movement behavior data set
a data set that is about the human daily movement behavior of the individual huamns in a given population.
human daily movement data set
potentially infectious contact process data set in a population
a data set that is about one or more potentially infectious contact processes in a population of host organisms.
contact data set
potentially infectious contact data set
infectious disease control strategy census
a census of infectious disease control strategies put into place to reduce infection acquisitions that are part of an infection in an ecosystem.
control strategy census
school closure infectious disease control strategy census
an infectious disease control strategy census that is about school closure infectious disease control strategies implemented in a particular geographical region.
This class represents datasets about strategies for school closure. Datasets about individual actual school closures go elsewhere.
school closure control strategy census
vaccination infectious disease control strategy census
This class is an inventory of vaccination control strategies, not vaccinations themselves. So it should be a list of things like "Publix vaccination plan", "Alachua county vaccination plan", "Sam's Club vaccination plan", etc. And not a list of individual vaccinations given to actual patients (see population vaccination census)
vaccination control strategy census
population vaccination census
vaccine / immunization registry data, vaccination / immunization records extracted from an EHR
a population treatment census that is about one or more vaccinations of organisms in a population.
vaccination census
vaccination administration census
dataset about excess mortality in a population
A population mortality dataset that compares deaths in the population during one time interval to deaths in the population during a previous time interval and reports an estimate of how many more or less deaths occurred in the later time interval.
Often used during epidemics or pandemics to estimate the death toll.
excess mortality dataset
census of supplies of vaccine products
A control strategy inventory census that counts available vaccine doses of one or more similar vaccines.
vaccine availability
Motivated my MIDAS coordination center indexing of COVID-19 data, software, etc. By "similar vaccines" we typically mean same pathogen, but could be similar in other ways (requiring refrigeration of a certain kind).
census of vaccination supplies
census of facilities that conduct clinical laboratory tests
A census of facilities that conduct clinical laboratory testing.
testing availability
The census might also include information about each facility such as operating hours, address, accessibility, and so on.
laboratory testing facility census
model for disease transmission parameter estimation
An algoirthm that is used to estimate the "true" values of certain parameters of disease transmission and/or forecasting.
Examples of parameters estimated include R0, transmissibility, infectious period.
parameter estimation model
An algorithm that operates on a representation of some portion of reality and that representation has a structure with nodes that stand for certain entities and edges that state some direct or indirect relationship between pairs of entities.
The algorithm might involve also generating or creating the network structure in addition to operating on it.
network model
laboratory testing capacity action specification
An action specification giving the number of laboratory tests of a certain type that it is possible to perform in a given population during a specific time interval.
laboratory testing capacity
data set about Earth's atmospheric weather
A data set about the Earth's atmospheric weather
weather data set
monkeypox disease inhering in a human being
A monkeypox disease inhering in a human being.
requested by MIDAS CC
human monkeypox
epidemic simulator action specification
infectious disease control strategy action specification
individual treatment control strategy action specification
creating a data set
A planned process that has a data set as its specified output.
data set creation
dataset creation
dataset creating
creating a copyright license
A planned process that has a copyright license as its specified output.
copyright license creation
Note: for less than 24 hours, this class was a bit more specific to software licenses, but it did not have the equivalent class axiom during that time.
copyright license for a creative work
A document that is about the legal rights, claims, and obligations of a legal person (person or organization) under copyright law, and how that legal person intends for those rights, claims, and obligations to be handled/managed by users of the creative work to which this document is attached.
Can be for any creative work including fiction. But the license itself is an ICE, and refers to real claims and obligations.
copyright license
data service software application
A software application that implements a data service.
data service software
TODO
facultative role
A role borne by an organism in virtue of the fact that it is in intimate association with one or more organisms of different species, and is realized by bodily benefit to that organism as an occurrent part of a symbiosis with the other organisms. This bodily benefit takes the place of the organism or some relatively isolated part of the organism realizing some normal homeostasis disposition itself.
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
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host.
history
The usage or intended usage of a drug product to act against a viral infection of a host.
antiviral drug
A viral infectious disease that has_material_basis in Zika virus, which is transmitted_by Aedes aegypti mosquitoes and targets neural progenitor cells and neuronal cells in all stages of maturity and has_symptom fever, has_symptom rash, has_symptom headaches and has_symptom joint pain.
Zika fever
A viral infectious disease that results_in infection, has_material_basis_in Dengue virus [NCBITaxon:12637] with four serotypes (Dengue virus 1, 2, 3 and 4), which are transmitted_by Aedes mosquito bite. The infection has_symptom fever, has_symptom severe headache, has_symptom severe pain behind the eyes, has_symptom joint pain, has_symptom muscle and bone pain, has_symptom rash, and has_symptom mild bleeding.
A dengue disease that occurs when a person experiences a second infection with a heterologous Dengue virus serotype, which is transmitted_by Aedes mosquito bite. The infection has_symptom hemorrhagic lesions of the skin, has_symptom thrombocytopenia, has_symptom reduction in the fluid part of the blood, and has_symptom high fever.
A viral infectious disease that results in infection of primates, rodents and humans, located in skin, has_material_basis_in Monkeypox virus, which is transmitted by contact with the animal's blood, body fluids, rash, or with the body fluids of a sick person, transmitted by fomites, and transmitted by respiratory droplets. The infection has symptom fever, has symptom muscle ache, has symptom headache, and has symptom lymphadenopathy.
A viral infectious disease that results_in infection, located_in respiratory tract, has_material_basis_in Influenzavirus A, has_material_basis_in Influenzavirus B, or has_material_basis_in Influenzavirus C, which are transmitted_by droplet spread of oronasal secretions during coughing, sneezing, or talking from an infected person. It is a highly contagious disease that affects birds and mammals and has_symptom chills, has_symptom fever, has_symptom sore throat, has_symptom runny nose, has_symptom muscle pains, has_symptom severe headache, has_symptom cough, and has_symptom weakness.
Influenza with non-respiratory manifestation (disorder)
Influenza with other manifestations (disorder)
Influenza with other manifestations NOS (disorder)
influenza with non-respiratory manifestation
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
drug product
A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.
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.
An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system.
A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional.
Water vapour is a vapour which is the gas phase of water.
Perhaps a better relation between water vapour and water can be found in or added to RO?
Atmospheric water vapour is water vapour that is part of an atmosphere.
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)
hydrological precipitation process
A temperature that inheres in some portion of air.
Draft class. In discussion in Issue #278.
air temperature
A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely.
This class is to be populated by inference.
gaseous environmental material
Environmental variability which inheres in an astronomical body part or in outer space.
This class refers to all weather, including atmospheric and space weather. Please use a subclass for more specificity.
weather
This class refers to the common usage of "weather", referencing the state of a (part of) an astronomical body's atmosphere.
atmospheric weather
A condition which inheres in an environmental system by virtue of that system undergoing variation in its composition, the distribution of the qualities its components bear, and/or in the processes which occur within it and which it participates in.
This class is very general, but the nature of environmental variability is indeed quite variable. This class may be refined once we have more subclasses to consider.
environmental variability
Should environmental feature become something more towards a disposition, the assert would be updated to something like "has participant (environmental system or (material entity and has disposition some environmental feature))". There are several issues surrounding the reconcilliation of environmental feature and environmental system, both theoretical and practical.
environmental system process
The temperature of a environmental material.
A molecular assay that is used to analyze metagenomic data; genetic material recovered directly from environmental samples for genomic research.
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.
A publication issued on a regular, ongoing basis containing separate research articles and other writings such as reviews, comments and conference reports.
definition is circular.
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.
The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.
reproduction
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
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.
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.
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.
The emergence of an adult insect from a pupa case.
eclose
eclosion
The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
The reproductive process in which the parent is separated from its offspring either by giving birth to live young or by laying eggs.
aging
The internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes.
biological_process
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
biological process
An aging process that has as participant a whole multicellular organism. Multicellular organism aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Multicellular organisms aging includes processes like cellular senescence and organ senescence, but is more inclusive. May precede death (GO:0016265) of an organism and may succeed developmental maturation (GO:0021700).
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.
oviposition
The process in which a virus effects a change in the structure or processes of its host organism.
modulation by virus of host anatomical structure or process
modulation by virus of host anatomy or process
modulation by virus of host morphology or physiology
The set of viral processes that induce an apoptotic process in infected host cells, facilitating release and spread of progeny virions.
activation by virus of host apoptotic programmed cell death
activation of apoptosis in host by virus
induction by virus of host apoptotic programmed cell death
induction by virus of host apoptotic process
The process in which a virus effects a change in the processes and activities of its host organism.
modification by virus of host cellular process
regulation by virus of host cellular process
regulation of cellular process in host by virus
regulation of host cellular process by virus
modulation of cellular process in host by virus
reproductive behavior
A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
developmental process
The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
multicellular organismal reproductive behavior
Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group.
Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior.
The process in which an organism effects a change in the structure or processes of a second organism.
regulation of morphology of other organism
regulation of physiological process of other organism
regulation of physiology of other organism
regulation of morphology or physiology of other organism
modification of morphology or physiology of other organism
Any process in which a virus increases the frequency, rate or extent of host cysteine-type endopeptidase activity (also called caspase activity) which contributes to the apoptotic process.
induction by virus of host caspase activity
induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process
Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
regulation of non-apoptotic programmed cell death
The process in which a symbiont organism effects a change in the structure or processes of its host organism.
modification by symbiont of host morphology or physiology
Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
entry into host
Any process in which an organism has an effect on an organism of a different species.
interspecies interaction between organisms
A process in which an organism modulates the frequency, rate or extent of programmed cell death in a second organism.
modulation of programmed cell death in other organism
A biological process that directly contributes to the process of producing new individuals, involving another organism.
The specific behavior of an organism that is associated with reproduction involving another organism of the same or different species.
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.
reproductive process in a multicellular organism
multicellular organismal reproductive process
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
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.
regulation of cellular physiological process
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
establishment of localization
The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location.
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.
A biological process which involves another organism of the same or different species.
multi-organism process
Any process in which an organism has a behavioral effect on another organism of the same or different species.
behavioral interaction between organisms
behavioral interaction with other organism
behavioural interaction between organisms
behavioural interaction with other organism
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.
regulation of morphology of other organism during symbiotic interaction
regulation of physiological process in other organism during symbiotic interaction
regulation of physiology of other organism during symbiotic interaction
modification of morphology or physiology of other organism during symbiotic interaction
modulation of morphology or physiology of other organism during symbiotic interaction
regulation of morphology or physiology of other organism during symbiotic interaction
modification of morphology or physiology of other organism involved in symbiotic interaction
Any process in which an organism modulates the frequency, rate or extent of programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
modulation by symbiont of host non-apoptotic programmed cell death
modulation by symbiont of host programmed cell death
Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
activation by organism of host programmed cell death
activation by organism of programmed cell death in other organism during symbiotic interaction
enhancement of host programmed cell death
enhancement of host programmed cell death by organism
induction by organism of programmed cell death in other organism involved in symbiotic interaction
induction by symbiont of host programmed cell death
upregulation by symbiont of host programmed cell death
activation by organism of non-apoptotic programmed cell death in other organism
activation by symbiont of host programmed cell death
induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction
positive regulation by symbiont of host non-apoptotic programmed cell death
stimulation by symbiont of host programmed cell death
induction by organism of programmed cell death in other organism during symbiotic interaction
induction of non-apoptotic programmed cell death by other organism
positive regulation by symbiont of host programmed cell death
Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death in the host, where programmed cell death proceeds by apoptosis. The host is defined as the larger of the organisms involved in a symbiotic interaction.
activation by organism of host apoptosis
activation by organism of host apoptotic programmed cell death
induction by organism of host apoptotic programmed cell death
positive regulation by organism of host apoptotic programmed cell death
up regulation by organism of host apoptotic programmed cell death
up regulation by symbiont of host apoptosis
up-regulation by organism of host apoptotic programmed cell death
up-regulation by symbiont of host apoptosis
upregulation by organism of host apoptotic programmed cell death
upregulation by symbiont of host apoptosis
activation by symbiont of host apoptosis
positive regulation by symbiont of host apoptosis
stimulation by symbiont of host apoptosis
Note that term is to be used to annotate gene products in the symbiont. To annotate host gene products, consider the biological process term 'positive regulation of apoptosis ; GO:0043065'.
positive regulation by symbiont of host apoptotic process
Any process in which an organism modulates the frequency, rate or extent of programmed cell death in a second organism, where the two organisms are in a symbiotic interaction.
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
modulation of programmed cell death in other organism involved in symbiotic interaction
Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death by apoptosis in a second organism, where the two organisms are in a symbiotic interaction.
induction by organism of apoptosis in other organism involved in symbiotic interaction
activation by organism of apoptosis in other organism during symbiotic interaction
positive regulation by organism of apoptosis in other organism involved in symbiotic interaction
positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction
stimulation by organism of apoptosis in other organism during symbiotic interaction
activation by organism of apoptotic programmed cell death in other organism during symbiotic interaction
induction by organism of apoptosis in other organism during symbiotic interaction
induction by organism of apoptotic programmed cell death in other organism during symbiotic interaction
positive regulation by organism of apoptosis in other organism during symbiotic interaction
positive regulation by organism of apoptotic programmed cell death in other organism during symbiotic interaction
up regulation by organism of apoptosis in other organism during symbiotic interaction
up-regulation by organism of apoptosis in other organism during symbiotic interaction
upregulation by organism of apoptosis in other organism during symbiotic interaction
Any viral process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
positive regulation of apoptosis by virus
positive regulation of apoptotic process by virus
Any viral process that modulates the rate or extent of progression through the cell cycle.
viral process regulating host cell cycle
post-mating oviposition
Any process that modulates a measurable attribute of any biological process, quality or function.
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.
organism emergence from protective structure
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
objective specification
purpose of a study; support of hypothesis, discovery of new information
a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
OBI Plan and Planned Process/Roles Branch
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
OBI Plan and Planned Process branch
action specification
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
software
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
PERSON: Chris Stoeckert
GROUP: OBI
Data items include counts of things, analyte concentrations, and statistical summaries.
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
data
data item
symbol
a smallish, word-like datum...
20091104, MC: this needs work and will most probably change
PERSON: Jonathan Rees
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
10 feet. 3 ml.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
scalar measurement datum
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
directive information entity
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
person:Allyson Lister
person:Chris Stoeckert
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
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
measurement datum
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
version number
A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
A scalar measurement datum that is the result of measuring a temporal interval
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
time measurement datum
time stamped measurement datum
pmid:20604925 - time-lapse live cell microscopy
A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
experimental time series
time sampled measurement data set
"Behaviour related to the activity which primary purpose is the sexual reproduction." [NBO:GVG]
Mus musculus
House mouse
Virus
Poxviridae
Chordopoxvirinae
Orthopoxvirus
Mirela L Vasconcelos
monkey pox virus
Monkeypox virus
Variola virus
H5N1 subtype of Influenza A virus
H5N1 subtype
Aedini
Reoviridae
Rotaviruses
Rotavirus
Togaviridae
Alphavirus
eastern equine encephalomyelitis virus EEEV
Flaviviridae
Flavivirus
Dengue virus group
Dengue virus 1
Dengue virus 2
Dengue virus 3
Dengue virus 4
Hepatitis C virus group
Hepatitis C viruses
Hepatitis C-like viruses
Hepacivirus
hepatitis C virus HCV
human hepatitis C virus
human hepatitis C virus HCV
human hepatitis virus C HCV
post-transfusion hepatitis non A non B virus
Hepatitis C virus
Coronaviridae
Chlamydia/Chlamydophila group
Mononegavirales
Paramyxoviridae
Paramyxovirinae
Morbilliviruses
Morbillivirus
Measles virus
Pneumovirinae
Pneumoviridae
Pneumovirus
Filoviridae
Rhabdoviridae
Lyssavirus
Rabies virus
Rabies lyssavirus
Orthomyxoviridae
Influenza A virus
H1N1 subtype of Influenza A virus
H1N1 subtype
H2N2 subtype of Influenza A virus
H2N2 subtype
Influenza virus type B
Influenza B virus
Bunyaviridae
Phleboviruses
Phlebovirus
Rift Valley fever virus
Retroviridae
Lentivirinae
Lentivirus
Primate immunodeficiency viruses
Primate lentivirus group
HIV-1
Human immunodeficiency virus type 1
human immunodeficiency virus 1 HIV-1
human immunodeficiency virus HIV-1
human immunodeficiency virus type 1 HIV 1
human immunodeficiency virus type 1 HIV-1
human immunodeficiency virus type 1 HIV1
human immunodeficiency virus type 1, HIV-1
human immunodeficiency virus type I HIV-1
human immunodeficiency virus type-1 HIV-1
human immunodeficiency virus-1 HIV-1
Human immunodeficiency virus 1
HIV type 2
HIV-2
Human immunodeficiency virus type 2
Human immunodeficiency virus-2
human immunodeficiency virus type 2 HIV-2
human immunodeficiency virus type 2, HIV-2
Human immunodeficiency virus 2
Teleostomi
bony vertebrates
Euteleostomi
H3N2 subtype of Influenza A virus
H3N2 subtype
H7N2 subtype of Influenza A virus
H7N2 subtype
H7N7 subtype of Influenza A virus
H7N7 subtype
H5N2 subtype of Influenza A virus
H5N2 subtype
Caliciviridae
Picornaviridae
Enterovirus
Ecdysozoa
Human poliovirus type 1
Poliovirus type 1
poliovirus type 1 PV1
Human poliovirus 1
Human poliovirus type 3
Poliovirus type 3
Human poliovirus 3
Hepatovirus
Hepatitis A virus
Hepatovirus A
Aphthovirus
Foot and mouth disease virus
foot and mouth disease virus FMDV
foot-and-mouth disease virus FMDV
Foot-and-mouth disease virus
Alphaproteobacteraeota
purple bacteria
purple bacteria and relatives
purple non-sulfur bacteria
purple photosynthetic bacteria
purple photosynthetic bacteria and relatives
Proteobacteria
Proteobacteria gamma subdivision
Purple bacteria, gamma subdivision
gamma proteobacteria
gamma subdivision
gamma subgroup
Gammaproteobacteria
Gram-postive bacterium
Firmicutes
Hepatitis D virus
hepatitis delta virus HDV
Hepatitis delta virus
Dengue virus
Staphylococcus
Aurococcus
Vibrio cholerae serogroup O1
Vibrio cholerae O1
Staphylococcus aureus
Micrococcus aureus
Micrococcus pyogenes
Staphlococcus pyogenes citreus
Staphylococcus pyogenes aureus
Streptococcus aureus
respiratory syncytial virus RS
respiratory syncytial virus RS virus
respiratory syncytial virus RSV
Respiratory syncytial virus
Streptococcaceae
Streptococcus
Diplococcus pneumoniae
Micrococcus pneumoniae
Streptococcus pneumoniae
Middle East respiratory syndrome coronavirus
Dipnotetrapodomorpha
Vibrionaceae group
Vibrionales
Pasteruellaceae group
Pasteurellales
Bacillales
Bacillus
Coxsackievirus A
Enterovirus EV-A
Human coxsackievirus A
Human enterovirus A
Enterovirus A
Enterovirus EV-C
Human enterovirus C
Poliovirus
Enterovirus C
Enterovirus D
Bacillus cereus var. anthracis
Bacteridium anthracis
anthrax
anthrax bacterium
Bacillus anthracis
Norwalk-like viruses
Norovirus
Boreoeutheria
Rhinovirus A
Bacillus difficilis
Clostridium difficile
Peptoclostridium difficile
Clostridioides difficile
ducks, geese, chickens, fowl, quail, currasows and allies
Listeria monocytogenes subsp. perhaemolytica
Plasmodiidae
Actinomycetes
High GC gram-positive bacteria
Actinobacteria
Mycobacteriaceae
Mycobacterium Lehmann and Neumann 1896
Mycobacterium
Bacillus tuberculosis
Bacterium tuberculosis
Mycobacterium tuberculosis typus humanus
Mycobacterium tuberculosis var. hominis
Mycobacterium tuberculosis
SFV complex
PVC group
Terrabacteria group
Ebola-like virus
Ebolavirus
Zaire ebolavirus
Ebola virus Reston
REBOV
Reston Ebola virus
Reston ebolavirus
Ebolavirus Sudan
SEBOV
Sudan Ebola virus
Sudan ebolavirus
CIEBOV
Côte d'Ivoire Ebola virus
Côte d'Ivoire ebolavirus
Ivory Coast ebolavirus
Tai Forest ebolavirus
Clostridia
Clostridiales
Clostridium cluster XI
Peptostreptococcaceae
Bacillaceae
Lactobacillales
Clostridioides
Rift Valley fever phlebovirus
Pancrustacea
Mandibulata
Influenzavirus A
Influenzavirus B
Crimean-Congo hemorrhagic fever nairovirus
Crimean-Congo hemorrhagic fever orthonairovirus
Bacteria
'Actinobacteria'
not Actinobacteria Cavalier-Smith 2002
Chlamydaeota
Chlamydiae
Chlamydiia
Neisseriales
Helicobacter
Campylobacter pylori
Campylobacter pylori subsp. pylori
Campylobacter pyloridis
Helicobacter nemestrinae
Helicobacter pylori
Campylobacterales
SARS coronavirus
H5N8 subtype of Influenza A virus
H5N8 subtype
Eukaryota
Proteobacteria beta subdivision
Purple bacteria, beta subdivision
beta proteobacteria
beta subdivision
beta subgroup
Betaproteobacteria
PEDV
Porcine epidemic diarrhea virus
Bacillus cholerae-suis
Salmonella cholerae-suis
Salmonella choleraesuis
Salmonella enterica ser. choleraesuis
Salmonella enterica
Proteobacteria epsilon subdivision
Purple bacteria, epsilon subdivision
epsilon proteobacteria
epsilon subdivision
epsilon subgroup
not Epsilobacteria
Epsilonproteobacteria
Spondweni virus group
Schistosomatoidea
blood flukes
Schistosomatidae
Euarchontoglires
Anthropoidea
Simiiformes
Cercopithecoidea
tetrapods
Tetrapoda
amniotes
Amniota
authority: Theria Parker & Haswell, 1897
Theria
Orthoretrovirinae
H5N6 subtype of Influenza A virus
H5N6 subtype
Opisthokonta
Metazoa
Bilateria
Protostomia
H7N9 subtype of Influenza A virus
H7N9 subtype
Neoptera
Endopterygota
deuterostomes
Deuterostomia
alveolates
Alveolata
Euglenozoans
Euglenozoa
Rickettsieae Philip 1957 (Approved Lists 1980) emend. Brenner et al. 1993
dsDNA virus, no RNA stage
Retroid viruses
Retro-transcribing viruses
ssRNA positive-strand viruses, no DNA stage
ssRNA negative-strand virus
dsRNA nonenveloped viruses
dsRNA viruses
malaria parasite p. ovale
Plasmodium ovale
Chikungunya virus
Haplorrhini
Deltavirus
mammals
Mammalia
plasmodium
Plasmodium (Plasmodium)
laverania
Plasmodium (Laverania)
Culicoidea
hematozoa
Aconoidasida
Enterovirus D68
Culicomorpha
Culicinae
ssRNA virus
Picornavirales
Acinetobacteraceae
Branhamaceae
Moraxellaceae
Acinetobacter
Acinetobacter genomosp. 2
Acinetobacter genomospecies 2
Bacterium anitratum
Acinetobacter baumannii
Schizotrypanum
Neisseriaceae
"Gonococcus" Lindau 1898
"Merismopedia" Zopf 1885
Gonococcus
Neisseria
Diplococcus gonorrhoeae
Gonococcus neisseri
Merismopedia gonorrhoeae
Micrococcus der gonorrhoe
Micrococcus gonococcus
Micrococcus gonorrhoeae
Neisseria gonorrhoeae
Diplokokkus intracellularis meningitidis
Micrococcus intracellularis
Micrococcus meningitidis
Micrococcus meningitidis cerebrospinalis
Neisseria weichselbaumii
Neisseria meningitidis
Insecta
Alcaligenaceae
Chlamydiales
Bordetella
Bacterium tussis-convulsivae
Hemophilus pertussis
Microbe de la coqueluche
Bordetella pertussis
Stegomyia
Enterobacteraceae
Enterobacteriaceae
Bacterium paratyphi
Bacterium paratyphi typhus A
Salmonella choleraesuis choleraesuis (serotype paratyphi A)
Salmonella choleraesuis subsp. choleraesuis serovar Paratyphi A
Salmonella paratyphi
Salmonella paratyphi A
Salmonella paratyphi-a
Salmonella enterica subsp. enterica serovar Paratyphi A
Escherichia
Bacillus coli
Bacterium coli
Bacterium coli commune
E. coli
Enterococcus coli
Escherichia coli
Kinetoplastea
Protomonadida
kinetoplasts
Kinetoplastida
Trypanosomatidae
Ebolavirus bundibugyo
Bundibugyo ebolavirus
Trypanosoma
Trypanosoma cruzi
apicomplexans
Apicomplexa
haemosporidians
haemosporina
Haemosporida
Plasmodium
malaria parasite P. falciparum
plasmodium (laverania) falciparum
Plasmodium falciparum
malaria parasite p. vivax
Plasmodium vivax
Plasmodium malariae
Salmonella
Salmonella cholerae-suis subsp. cholerae-suis
Salmonella choleraesuis subsp. choleraesuis
Salmonella enterica I
Salmonella enterica subsp. I
Salmonella enterica subsp. enterica
Eumetazoa
flatworms
Platyhelminthes
Trematoda
flukes
Digenea
Strigeidida
Schistosoma
Schistosoma mansoni
Schistosoma haematobium
Yersinia pseudotuberculosis subsp. pestis
Vibrionaceae
Zika virus
Beneckea
Listonella
Microspira
Pacinia
Vibrio
Arthropoda
Bacillo virgola del Koch
Bacillus cholerae
Bacillus cholerae-asiaticae
Kommabacillus
Liquidivibrio cholerae
Microspira comma
Pacinia cholerae-asiaticae
Spirillum cholerae
Spirillum cholerae-asiaticae
Vibrio cholera
Vibrio cholerae Pacini 1854
Vibrio cholerae-asiaticae
Vibrio comma
Vibrio cholerae
not Thiobacteria
delta/epsilon subdivisions
Sedoreovirinae
Coronavirinae
Coronavirus group 1
Group 1 species
Alphacoronavirus
Betacoronavirus
Hexapoda
Pasteurellaceae
Diptera
Nematocera
mosquitos
Culicidae
Aedes
Stegomyia aegypti
Aedes aegypti
Pseudomonaceae/Moraxellaceae group
Pseudomonadales
Helicobacter group
Helicobacteraceae
Campylobacteraceae Vandamme and De Ley 1991
Haemophilus
Bacterium influenzae
Coccobacillus pfeifferi
Haemophilus meningitidis
Influenza-bacillus
Mycobacterium influenzae
Haemophilus influenzae
Pterygota
Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Brenner et al. 1993
Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Dumler et al. 2001
Anaplasma Theiler 1910 (Approved Lists 1980) emend. Dumler et al. 2001
Nidovirales
chordates
Chordata
vertebrates
authority: Vertebrata Cuvier, 1812
Vertebrata
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
jawed vertebrates
Gnathostomata
"Dermacentroxenus rickettsii" Wolbach 1919
Rickettsia rickettsii (Wolbach 1919) Brumpt 1922
Burkholderia/Oxalobacter/Ralstonia group
Burkholderiales
Chlamydiaceae
Bedsonia
Chlamydophila
Miyagawanella
Rakeia
Rickettsiaformis
Chlamydia
Chlamydozoon trachomatis
Rickettsia trachomae
Rickettsia trachomatis
Chlamydia trachomatis
Sarcopterygii
Corynebacterineae
Corynebacteriales
Dicondylia
Bacillus cereus group
Panarthropoda
Craniata
Bacillus typhi
Bacterium (subgen. Eberthella) typhi
Salmonella choleraesuis serovar Typhi
Salmonella choleraesuis typhi
Salmonella enterica ser. typhi
Salmonella enterica serotype Typhi
Salmonella enterica serovar Typhi
Salmonella typhi
Salmonella enterica subsp. enterica serovar Typhi
Staphylococcaceae
Staphylococcus group
Acinetobacter calcoaceticus/baumannii complex
Bacillus/Lactobacillus/Strptococcus group
Firmibacteria
Bacilli
Enterobacteriaceae and related endosymbionts
Enterobacteriaceae group
Enterobacteriales
Enterobacterales
whales, hippos, ruminants, pigs, camels etc.
Placentalia
eutherian mammals
placental mammals
placentals
Eutheria
Anaplasmataceae Philip 1957 (Approved Lists 1980) emend. Dumler et al. 2001
"Ehrlichia (subgen. Cowdria)" Moshkovski 1945
"Rickettsia (subgen. Ehrlichia)" Moshkovski 1937
Ehrlichia Moshkovski 1945 (Approved Lists 1980) emend. Dumler et al. 2001
Primata
primate
primates
Primates
Ehrlichia chaffeensis Anderson et al. 1992 emend. Dumler et al. 2001
agent of human granulocytic ehrlichiosis
Catarrhini
Old World monkeys
monkey
monkeys
Cercopithecidae
Cercopithecinae
macaque
macaques
Macaca
Rhesus monkey
rhesus macaque
rhesus macaques
rhesus monkeys
Macaca mulatta
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.
contraindication
planned process
Injecting mice with a vaccine in order to test its efficacy
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
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.
intervention design
PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
Philppe Rocca-Serra
OBI branch derived
data encoding
storage of measurement results from an assay into a text file, such as
a documenting process to encode an information entity into a digital document
We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An 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.
averaging objective
A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
James Malone
scattered molecular aggregate
the sodium and chloride ions in a glass of salt water
a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
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
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.
2009-02-28: work on this term has been finalized during the OBI workshop winter 2009
center value
A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
average value
For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities.
A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix.
WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html
A voltmeter is a measurement device which is intended to perform some measure function.
A device is a processed material which is designed to perform some function or functions
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.
A group of linked computers, working together closely so that in many respects they form a single computer.
providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony
A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
environmental history design
A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.
disease state design
A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress.
MO_902 disease_state_design
pathogenicity design
A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.
MO_807 pathogenicity_design
Data analysis service such statistical abalysis or storage service such data backup.
A service that has some information content entity as input and output.
Information content entity was used as specified input and output since it was more appropriate then data item or dataset.
The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.
A scalar measurement datum that represents the number of events occuring over a time interval
investigation description
A textual entity that describes an investigation.
Person: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
project description
investigation identifier
A CRID symbol used to identify an investigation.
Person: Chris Stoeckert, Jie Zhneg
project ID
grant identifier
A CRID symbol used to identify a grant.
grant ID
Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/ar\ ticles/PMC4090399/
The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic re\ view. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/
A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according \ to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were no\ t justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed.
digital object identifier
The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073
A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles.
Discussed on Aug 22, 2016 OBI dev call. Details see tracker: https://sourceforge.net/p/obi/obi-terms/818/
https://en.wikipedia.org/wiki/Digital_object_identifier https://www.doi.org/
organism
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.
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A data transformation is a process which produces output data from input data
Elisabetta Manduchi
Helen Parkinson
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
data transformation objective
normalize objective
A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed.
PERSON: James Malone
averaging data transformation
An averaging data transformation is a data transformation that has objective averaging.
observation design
PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
A data item that was generated on the basis of a calculation or logical reasoning
BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted.
APOLLO DEVELOPERS: We need to check whether OBI changes the label and the hierarchical place of this class.
calculated datum
predicted data item
digital curation
PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44.
Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally.
computer
Apple PowerBook, Dell OptiPlex
A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions.
Trish Whetzel
study design
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
time series design
PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources.
Groups of assays that are related as part of a time series.
Philippe Rocca-Serra on behalf of MO
MO_887
A planned process that realizes the concretization of a software.
software execution
A software execution that is provided by the web service, and involves invoking software execution over network.
A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.
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.
A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
A clinically abnormal phenotype.
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
Barry Smith
Richard H. Scheuermann
Werner Ceusters
Scheuermann RH, Ceusters W, Smith B. Toward an ontological treatment of disease and diagnosis. Summit on translational bioinformatics. 2009;2009:116. Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/
A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
The totality of all processes through which a given disease instance is realized.
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.
A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
Apollo-SV currently defines two subclasses of treatment. See vaccination and antiviral treatment.
A processual entity which has as parts all the processes in which a given organism is participant.
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
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
A part of a disease course that occurs after an incomplete remission and that is similar to earlier parts of the disease course.
relapse
A CRID that constitutes a reference to an Internet resource.
uri
unique resource locator
A social role inhering in a human being.
human social role
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.
gender role
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.
male gender
male gender role
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.
female gender
female gender role
A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis.
health care role
human health care role
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.
patient
patient role
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).
health care provider organization role
An object aggregate of organisms.
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.
Any arbitrary collection of organisms. They need not be of the same taxonomic class.
collection of organisms
An object aggregate all of whose components are human beings.
collection of humans
A role inhering in an entity realized by social interactions in human society.
Previous definition: A role played by an entity in human social processes.
role in human social processes
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.
organization social role
A role in human social processes that inheres in an organism.
William R. Hogan Mathias Brochhausen
Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc.
Previous definition: A role in human social processes played by an organism.
organism social role
An organization social role that is realized by a health care process.
Previous definition: An organization social role played by an organization in health care processes.
organization health care role
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.
aggregate of organizations
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.
aggregate of sovereign states
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.
aggregate of geopolitical organizations
aggregate of dependencies
aggregate of major administrative subdivisions
A function inhering in a facility that manifests by the facility participating in providing inpatient and outpatient healthcare to a patient population.
hospital function
A function inhering in a facility that manifests by the facility participating in providing formal education to a student population.
school function
A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care.
hospital role
An organization social role that inheres in an organization and is realized by providing formal education to students.
school role
An organization that is the bearer of a hospital role.
hospital organization
An organization that is the bearer of a school role.
school organization
A human social role that is realized by the process of formal education that the bearer undergoes.
student role
nursery school role
primary school role
A material entity that is a human made strcuture with firm connection between its foundation and the ground.
"Building" is a subclass of this.
This type of entity is referred to as "Bauwerk" or "Bauliche Anlage".
architectural structure
An architectural structure that bears some function.
facility
A facility that is run by a hospital organization and is the bearer of a hospital function.
hospital facility
A facility that is run by a school organization and is the bearer of a school function.
school facility
secondary school role
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.
Housing units are individuated by their residence functions.
housing unit
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.
household
workplace facility
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
workplace function
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.
racial identity datum
A facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population.
health care facility
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.
identity datum
A quality that is the extent of space between two entities.
biological sex
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
A physical quality of the thermal energy of a system.
female
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
male
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
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.
A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
A structural quality inhering in a bearer by virtue of the bearer's touching another entity.
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.
Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
A material entity that consists of two or more organisms, viruses, or viroids.
group of organisms
organism collection
May be of the same or different species.
PCO:collection of organisms
A collection of organisms, all of the same species, that live in the same place.
Still uncertain if this should include every organism of a species living in an area or any subset of them. For now make this a general term (unspecified) and then subclasses can be more specific.
It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across ontologies and only one term used.
population
A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species.
collection of organisms of the same species
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
AGB,PRS
effect size
effect size estimate
statistical sample size is a count evaluating the number of individual experimental units
AGB-PRS
statistical sample size
study group population size
specificity is a measurement datum qualifying a binary classification test and is computed by substracting the false positive rate to the integral numeral 1
specificity
true negative rate
sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1
recall
sensitivity
adapted from: http://en.wikipedia.org/wiki/Sensitivity_and_specificity and http://mathworld.wolfram.com/Sensitivity.html
true positive rate
Relative risk is a measurement datum which denotes the risk of an 'event' relative to an 'exposure'. Relative risk is calculated by forming the ratio of the probability of the event occurring in the exposed group versus the probability of this event occurring in the non-exposed group.
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
categorical variable
a variable is a data item which can assume any of a set of values, either as determined by an agent or as randomly occuring through observation.
STATO
adapted from wolfram-alpha (http://www.wolframalpha.com/input/?i=variable) definition 2. and from Oxford English Dictionary: http://www.oed.com/view/Entry/221514?redirectedFrom=variable#eid, definition B,1
variable
Probability distribution estimated empirically on the data without assumptions on the shape of the probability distribution.
Initially discussed at https://github.com/incf-nidash/nidm/pull/191
The weighted arithmetic mean is a measure of central tendency that is the sum of the products of each observed value and their respective non-negative weights, divided by the sum of the weights, such that the contribution of each observed value to the mean may defer according to its respective weight. It is defined by the formula: A = sum(vi*wi)/sum(wi), where 'i' ranges from 1 to n, 'vi' is the value of each observation, and 'wi' is the value of the respective weight for each observed value. The weighted arithmetic mean is a kind of mean similar to an ordinary arithmetic mean (the most common type of average), except that instead of each of the data points contributing equally to the final average, some data points are weighted, meaning they contribute more than others. The weighted arithmetic mean is often used if one wants to combine average values from samples of the same population with different sample sizes.
Orlaith Burke
https://docs.scipy.org/doc/numpy/reference/generated/numpy.average.html np.average(range(1,11), weights=range(10,0,-1))
weighted arithmetic mean
Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome.
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].
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]
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.
Editor note: changed label and definition to reflect CARO2
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.
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.
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
An anatomical structure that has more than one cell as a part.
A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.
A life cycle temporal boundary that marks the end of the life cycle of the organism.
unit
A unit which is a standard measure of physical quantity consisting of only a numerical number without any units.
dimensionless unit
A dimensionless ratio unit which denotes numbers as fractions of 100.
percent
A dimensionless unit which denotes an amount or magnitude of one quantity relative to another.
ratio
A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator).
fraction
A unit which represents a standard measurement occurrence of a process per unit time.
rate unit
A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine.
Many vaccines are developed to protect against infectious pathogens. Many vaccines are also being developed against some diseases such as cancer and autoimmune diseases. Vaccine is developed against a disease. Allergy.
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 contraindication is a contraindication that increases the risks of a vaccination.
vaccine function is a function that inheres in a vaccine that induces protective immune response against a disease. It is realized in the immunization process in the host.
PERSPN: Oliver He: There has been hot discussion about whether we use 'vaccine function' or 'vaccine role'. Vaccine role may not be the good term to use. Vaccine is designed to be 'vaccine', so it should be vaccine function. One special case is cowpox virus. The cowpox virus can be mixed with some liquid like water and used as a smallpox vaccine. In this case, people often say: the cowpox virus has a 'vaccine role'. However, the cowpox virus vaccine is a processed material of a mix of the virus with water. The virus is a virus, it is not a vaccine per se. Therefore, vaccine role may not be an accurate term.
vaccine preparation is a manufacturing process to produce a vaccine.
deprecated due to malformed URI and created anew.
obsolete specificity of case detection
obsolete specificity of treatment detection
obsolete sensitivity of treatment detection
Originally imported into Apollo-SV for purpose of indexing in OBC.ide news articles relevant to infectious disease epidemiology.
news article
Genomic data is data about the genomes of an organism.
Obsolete Class
organism population universal
atmosphere of the Earth
"A time unit which is equal to 7 days." [Wikipedia:Wikipedia]