An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.
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.
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
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
US State Two Digit Identifier
US State Two Letter Abbreviation
US State Ens Identifier
UN Numerical Code
ISO 3166-1-alpha-3 code
ISO 3166-1-alpha-2 code
Proposed Apollo Location Code
ISO 3166-2 code
geonameid
integer id of record in geonames database
geonames admin1 code
fipscode (subject to change to iso code), see exceptions below, see file admin1Codes.txt for display names of this code; varchar(20)
geonames admin2 code
code for the second administrative division, a county in the US, see file admin2Codes.txt; varchar(80)
geonames admin3 code
code for third level administrative division, varchar(20)
geonames admin4 code
code for fourth level administrative division, varchar(20)
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
editor preferred label
editor preferred term~editor preferred label
example
example of usage
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
definition editor
alternative label
alternative term
A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
definition source
Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
curator note
An administrative note of use for a curator but of no use for a user
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
ontology term requester
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
The 'term requester' can credit the person, organization or project who request the ontology term.
is denotator type
Relates an class defined in an ontology, to the type of it's denotator
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
Alan Ruttenberg
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
Chris Mungall
expand assertion to
ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
first order logic expression
antisymmetric property
part_of antisymmetric property xsd:true
Use boolean value xsd:true to indicate that the property is an antisymmetric property
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
has ID digit count
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
Person:Alan Ruttenberg
has ID range allocated
Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
has ID range allocated to
has ID policy for
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
has ID prefix
Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
has associated axiom(nl)
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
is allocated id range
Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
Add as annotation triples in the granting ontology
retired from use as of
relates a class of CRID to the date after which further instances should not be made, according to the central authority
In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp
has ontology root term
Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
Nicolas Matentzoglu
may be identical to
A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
David Osumi-Sutherland
VFB
Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
scheduled for obsoletion on or after
Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
Chris Mungall, Jie Zheng
GO ontology
has axiom id
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom label
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
ISA alternative term
NIAID GSCID-BRC alternative term
This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
logical characteristic of object property
'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . }
Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
temporal interpretation
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
an alternative term used for STATO statistical ontology and ISA team
Alejandra Gonzalez-Beltran
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
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
has broad synonym
has_definition
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
has exact synonym
An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
has narrow synonym
An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
has related synonym
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
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
obsolete_is_realized_by
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]
replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by'
is realized by
realized by
realized_by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
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
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t [XXX-001
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
is aggregate of
aggregate of
aggregate_of
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])
every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002])
if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001])
(forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002]
(forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002]
(forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001]
occupies spatial region at some time
exists at
[copied from inverse property 'part of continuant at all times that whole exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)
b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'.
[copied from inverse property 'part of continuant at all times that whole exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'
(iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001]
has continuant part at all times
b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has proper continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has proper continuant part@en(x,y,t)'.
has proper continuant part at all times
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
[copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant
[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region
[copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])
has spatial occupant at some time
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
b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'proper part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'proper part of continuant@en(x,y,t)'.
(iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001]
proper part of continuant at all times
[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
has participant at all times
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
Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
[copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.
BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
[copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'
b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001])
continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002])
continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001])
continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001])
continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001])
if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002])
(forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002]
(forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002]
(forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001]
(forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001]
(forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001]
(forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001]
(iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001]
part of continuant at all times
has proper temporal part
history of
has history
[copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
[copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)
This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'
[copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.
[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant
[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
[copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
has continuant part at all times that part exists
is in aggregate
A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1's jurisdiction falls within the relevant jurisdiction of G2.
'is subordinate authority of' Domain: governing organization Range: governing organization Formal properties: transitive, anti-symmetric, irreflexive Natural language definition: A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1 falls within the relevant jurisdiction of G2.
is subordinate authority of
It is not intended to be maximal, in the sense that if a has_jurisdiction_in b, and b is not part of c, then a NOT has_jurisdiction_in c. in other words, it is perfectly fine to say: a disjoint b c has_jurisdiction_in a c has_jurisdiction_in b otherwise, we'd end up creating some mereological sum of all the islands, contiguous land masses, etc. of the United States, calling it "United States territory", asserting United States has_jurisdiction_in United States territory, then figuring out all the parts of that territory like islands, etc. We'd end up doing the same thing for every sovereign state, major administrative subdivision (at least those like Hawaii that are multiple), etc. Seems like an unnecessary duplication of entities.
a governmental organization has jurisdiction in particular territories (areas of land), which means that it can make and enforce laws that govern peoples living in those territories.
if a has_jurisdiction_in b, then a has_jurisdiction_in all parts of b.
has jurisdiction in
has measurement unit label
A relation between a value specification and its unit of measurement.
The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend
c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense
see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
is_about is a (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
is about
An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
PERSON: Jonathan Rees
Person: Alan Ruttenberg
mentions
Inverse of the relation 'mentions'
mentioned by
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q
8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
is quality measurement of
inverse of the relation 'denotes'
Person: Jie Zheng, Chris Stoeckert, Mike Conlon
denoted by
relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
has coordinate unit label
relates a process to a time-measurement-datum that represents the duration of the process
is duration of
inverse of the relation of is quality measurement of
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
is quality measured as
A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality.
Person:Bjoern Peters
is quality specification of
inverse of the relation of is quality specification of
quality is specified as
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
has time stamp
relates a time stamped measurement datum to the measurement datum that was measured
has measurement datum
results_in
This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal.
owns
a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b.
Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.
is owned by
has_specified_input
see is_input_of example_of_usage
The inverse property of is_specified_input_of
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Alan Ruttenberg
is_specified_input_of
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has_specified_output
The inverse property of is_specified_output_of
is_specified_output_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
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
A relation between an information content entity and a value specification that specifies its value.
Reinach, A. S�mtliche Werke. Texkritische Ausgabe, M�nchen: Philosophia Verlag, 1989, p.189-204.
is administered by
is enrolled in school
is admitted to hospital
inheres in
this fragility inheres in this vase
this fragility is a characteristic of this vase
this red color inheres in this apple
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
has_participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
is concretized as
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
concretizes
is_concretization_of
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
disposition of
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
location_of
location of
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
located_in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
the surface of my skin is a 2D boundary of my body
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
2D_boundary_of
boundary of
is 2D boundary of
is boundary of
2D boundary of
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
has boundary
has_2D_boundary
has 2D boundary
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which ends
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
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 preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
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
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
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.
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
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has component
p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates
p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y
negatively regulates (process to process)
negatively regulates
p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
positively regulates (process to process)
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
capable of part of
'heart development' has active participant some Shh protein
OBSOLETE x has participant y if and only if x realizes some active role that inheres in y
x has participant y if and only if x realizes some active role that inheres in y
This may be obsoleted and replaced by the original 'has agent' relation
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
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporal relation
temporally related to
starts
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
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
x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
has start location
x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
has end location
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
has output
A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
results in formation of
p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
characteristic of part of
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
colocalizes with
a particular instances of akt-2 enables some instance of protein kinase activity
c enables p iff c is capable of p and c acts to execute p.
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
part of structure that is capable of
c involved_in p if and only if c enables some process p', and p' is part of p
involved in
enabled by
regulated by
negatively regulated by
positively regulated by
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
input of
output of
x spatially_coextensive_with y if and inly if x and y have the same location
This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
spatially coextensive with
causally downstream of
immediately causally downstream of
p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
indirectly positively regulates
p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
indirectly negatively regulates
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
causally upstream of
p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
immediately causally upstream of
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
inverse of causally upstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
directly positively regulates activity of
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
A relationship between a material entity and a process where the material entity has some causal role that influences the process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
molecular interaction relation helper property
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
causal relation between material entity and a process
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
directly positively regulates (process to process)
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
directly negatively regulates (process to process)
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
produces
a produced_by b iff some process that occurs_in b has_output a.
produced by
A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
acts upstream of or within, positive effect
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
causally upstream of or within, negative effect
causally upstream of or within, positive effect
DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information.
DEPRECATED inheres in
DEPRECATED bearer of
A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
realized in response to
Genetic information generically depend on molecules of DNA.
The novel *War and Peace* generically depends on this copy of the novel.
The pattern shared by chess boards generically depends on any chess board.
The score of a symphony g-depends on a copy of the score.
This pdf file generically depends on this server.
A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
Molecules of DNA are carriers of genetic information.
This copy of *War and Peace* is carrier of the novel written by Tolstoy.
This hard drive is carrier of these data items.
*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
is carrier of
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
indirectly causally upstream of
p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
indirectly regulates
A diagnostic testing device utilizes a specimen.
X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
See github ticket https://github.com/oborel/obo-relations/issues/497
device utilizes material
A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
obsolete has_disposition
negatively_regulates
NOTE: there appears to be some consistency in usage as to whether processes or continuants realize
obsolete_realized_by
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
A relation between a scalar measurement data item and a number that quantifies it.
The range should probably not be restricted to "float". It makes sense to set it to "real". However we do not know how this change will affect SPARQL queries, so we have left the range as-is for now.
has measurement value
has x coordinate value
has z coordinate value
has y coordinate 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 that has specified output a software product and that involves the creation of source code.
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
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
A continuous probability distribution whose characteristics and shape are determined by two parameters, alpha and beta.
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, and that realizes some concretization of a census objective specification.
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
host organism
A disease that inheres in a host and, when realized, is realized as a disease course that is causally preceded by an infection.
A disease that is caused by an infection.
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 and/or estimate all the organisms of a particular taxon in a particular geographical region or place and create a data set about them.
An objective specification to observe all the organisms of a particular taxon in a particular geographical region or place and create a data set about them.
Today, census taking typically consist of some mixture of counting the number of individuals in a population and estimating the numbers of subpopulations that are prone to overcounting or undercounting.
census objective specification
A plan specification with a census objective specification.
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 movement of organism
An action specification that delineates some minimum value or maximum value for some test statistic within a continuous probability distribution that is meant to serve as a lower bound or upper bound, respectively, for some population or sample of interest.
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 document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc.
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 forecasting software application
infectious disease forecaster
An investigation that realizes the concretization of some disease state design and that has as an occurrent part some population survey that has specified input some case definition.
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.
data set about Earth's atmosphere or some part of it
A data set that is about either the Earth's atmosphere or some part of the Earth's atmosphere.
atmospheric data set
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
A disease surveillance that detects evidence of the presence of pathogens in sewage.
sewage disease surveillance
See the CDC's explanation of wastewater surveillance, and how it uses the term 'wastewater' synonymously with 'sewage', here: https://www.cdc.gov/nwss/wastewater-surveillance.html.
wastewater disease surveillance
A count of simulated or physical individuals in a population.
population count
A disease surveillance data set that is about some wastewater disease surveillance.
sewage surveillance data
wastewater surveillance data set
A scalar measurement datum that is about some population and is normalized by unit land area in a particular geographical region.
population density datum
An individual treatment control strategy in which individuals maintain a certain distance from other individuals during a social act.
physical distancing infectious disease control measure
A place closure control strategy in which only selected places in a geographical region are permitted to stay open and travel is permitted only for people employed by certain organizations.
The places that are allowed to stay open are typically selected by the local or state government, and often include hospitals, many healthcare facilities, food stores and food banks, and law enforcement and emergency services.
lockdown infectious disease control measure
A count of cases in an epidemic that is about the entire temporal interval occupied by the epidemic.
A count of cases from the beginning of the epidemic until recently.
The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin.
cumulative epidemic case count
A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic.
A count of cases in an epidemic that spans a shorter interval, such as a particular day or a week.
Incident case counts are measured according to regular intervals, typically day or week.
incident epidemic case count
A count of processes in which a population and/or its members participate during a given temporal region.
A count of certain type of event that occurs within a population, such as deaths, infections, births, and so on during a particular time.
As the population is typically geographically defined (among other ways), the count is most often constrained to particular location in addition to a given time.
count of events occurring in a population
A count of death events that occurred in a population in a given temporal region.
population death count
count of deaths in a population
A count of vaccination events that occurred in a population during a temporal region.
population vaccination count
A count of vaccinations in a population during a particular time.
count of vaccinations in a population
A count of hospital stays in a population during a temporal region.
population hospitalization count
A count of hospitalizations in a population during a particular time.
count of hospital stays in a population
A count of infections (process) that occurred in a population in a given temporal region.
population infection count
A count of infections in a population during a particular time.
count of infections in a population
A cumulative infection count where the infections are an occurrent part of the same epidemic, and the reference interval is the interval occupied by the entire epidemic.
cumulative epidemic infection count
An incident infection count where the infections are an occurrent part of the same epidemic, and the temporal interval over which the count is made is a proper part of the reference interval.
incident epidemic infection count
A cumulative death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic.
cumulative epidemic death count
An incident death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval.
incident epidemic death count
A cumulative hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic.
cumulative epidemic hospitalization count
An incident hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval.
incident epidemic hospitalization count
A cumulative vaccination count where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the reference interval is the temporal interval occupied by the entire epidemic.
cumulative epidemic vaccination count
An incident vaccination count where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is a proper part of the reference interval.
incident epidemic vaccination count
An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization.
An intent to be vaccinated in the future.
intent to be vaccinated
An intentionality directed at future participation in a vaccination as the administrator of a vaccine or other immunization to an organism with an immune system.
An intention to give a vaccine to someone or an animal.
intent to vaccinate
A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab.
vaccination with nirsevimab
A count of vaccinations in a population that is the total number of a given type of vaccines administered during a reference temporal interval.
The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic or vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization.
cumulative vaccination count
A count of vaccinations in a population that is the number of a given type of vaccines administered during a proper occurrent part of a reference temporal interval.
The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization.
incident vaccination count
A count of infections in a population that is the total number of infections that occur during a reference temporal interval.
The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization.
cumulative infection count
A count of infections in a population that is the number of infections of a given type that occurred during a proper occurrent part of a reference temporal interval.
The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization.
incident infection count
A count of hospital stays in a population that is the total number of hospitalizations that occur during a reference temporal interval.
cumulative hospitalization count
A count of hospital stays in a population that is the number of hospital stays that occurred during a proper part of a reference temporal interval.
incident hospitalization count
A count of deaths in a population that is the total number of deaths that occur during a reference temporal interval.
cumulative death count
A count of deaths in a population that is the number of deaths that occurred during a proper part of a reference temporal interval.
incident death count
A count of disease cases that is the total number of individuals who come to meet the criteria of some case definition during a reference temporal interval.
cumulative case count
A count of cases in a population that is the number of individuals who come to meet the criteria of some case definition during a proper part of a reference temporal interval.
incident case count
guardian's intent to have a ward under their care vaccinated
An intentionality inhering in a person bearing a guardian role and that is directed at their future participation in an authorization for the vaccination or other immunization of a person under their care and who bears a ward role.
The intent of a guardian to have a ward under their care vaccinated in the near future.
Legally, this covers the situation of a parent intending to have their child vaccinated. That is because the parent(s) is(are) the natural gaurdian of the child. Other individuals appointed by a court as guardian are legal guardians. If the specific case of parent / child is required, we could create a subclass of this one where the guardian = parent of the ward, and ward = child. However, that could get into issues of adoption, etc. At the current time we do not have guardian role and ward role classes in OMRSE.
intent to have a ward vaccinated
organism reproduction
The process by which new organisms are created from existing ones.
reproduction
An intent to have a ward vaccinated where the guardian is a parent (natural or adoptive) and the ward is a child (natural or adopted) of that parent, and the parent has not otherwise been legally barred from making healthcare decisions for the child.
Intent to have one's child vaccinated.
The case of adult children is eliminated through the use of guardian and ward roles in the definition. The parent no longer has a guardian role, and the child no longer has a ward role, once the child is of legal age to make their own decisions. That is, those roles cease to exist.
intent to have a child vaccinated
epidemic simulator action specification
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.
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
two-dimensional spatial region
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal region
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable
realizable entity
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
zero-dimensional spatial region
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
characteristic
specifically dependent continuant
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object
fiat object part
an edge of a cube-shaped portion of space.
A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
one-dimensional spatial region
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries.
Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital
object aggregate
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
object
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
the boundary between the 2nd and 3rd year of your life.
p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
the temporal region during which a process occurs.
BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
Every continuant fiat boundary is located at some spatial region at every time at which it exists
(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
continuant fiat boundary
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
one-dimensional continuant fiat boundary
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
a marriage bond, an instance of requited love, an obligation between one person and another.
b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
relational quality
a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
two-dimensional continuant fiat boundary
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
zero-dimensional continuant fiat boundary
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host.
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
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.
An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii)
In some cases, geopolitical entities possess uninhabited geographical regions. However, it is that case that it controls the movement of people in and out of those regions, and its laws apply to those regions.
geopolitical entity
obsolete aggregate of governmental organizations
An aggregate of geopoliticial entities. Examples include the group of states of the United States, the nations of North America, and so on.
taken over by GEO_0000000401
obsolete group of governmental organizations
A geopolitical entity that is self contained and recognizes no higher political authority than itself.
nation
a governmental organization that has a local, regional, or territorial government that recognizes a sovereign state as its higher political authority
subnational entity
A subnational entity that is the primary organizational member of a nation, is subject to the full set of laws of the nation, enjoys all the privileges established under the laws of the nation, is not a member of any other geopolitical entity, and itself governs a part of the geographical region governed by the nation.
examples: Northern Ireland, Florida
major administrative subdivision
A subnational entity that does not possess full political independence or sovereignty as a sovereign state, but remains politically outside of the controlling state and controls a geographical region that is outside the controlling state's integral region.
Typically, the common feature is that the dependency does not conduct foreign affairs, and relegates this authority to the sovereign state. But otherwise, it is largely or completely autonomous relative to the administrative subdivisions. Examples include Puerto Rico (U.S.), Guam (U.S.), Greenland (Denmark), French Polynesia (France), and Falkland Islands (United Kingdom).
geopolitical dependency
An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common.
Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc.
aggregate of major administrative subdivisions
group of major administrative subdivisions
An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common.
Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies.
aggregate of dependencies
group of dependencies
subcontinental land mass
contiguous continental land mass
per the definition of 'contiguous' of "being in actual contact : touching along a boundary or at a point", these land masses share boundaries with other land masses that are part of the same continent, and thus are not surrounded by water like an island. At some point, we need an 'adjacent to' relation if BFO doesn't provide it. One question is whether this class encompasses fiat parts of islands.
contiguous land mass
An aggregate of organizations that is not itself a governmental organization, has only governmental organizations as members, and has at least two governmental organizations as members.
aggregate of governmental organizations
A subcontinental land mass that is part of an island and includes part of the land surface of the island.
It cannot be a part of the island, for example, that is below water.
contiguous island land mass
aggregate of contiguous land masses
geographical entity of astronomical body
A material entity that is (1) a bona fide or fiat object part of the crust, any bodies of liquid on or contained within the crust, or planetary boundary layer (if present) of a terrestrial planet (including Earth), dwarf planet, exoplanet, natural satellite, planetesimal, or small Solar System body, and that (2) overlaps the planetary surface (including having a boundary that coincides with part of the planetary surface).
Includes atmosphere, crust, geographical regions (e.g., the geographical region over which the state of Florida has jurisdiction), bodies of water, mountains, etc. Generally, an individual organism is a distinct object that is not a part of the Earth, although this requires more thought. But the intent is definitely for this class to NOT subsume organism universally. Human beings are contained within, but not part of, the Earth, for example.
Note that despite the word 'planetary' in 'planetary surface', it refers generally to surface of dwarf planets, asteroids, moons, etc.
We note that not all planets have a surface per se (e.g., gas giants such as Jupiter and Saturn). So only planets, natural satellites, etc. with a planetary surface (with or without a planetary boundary layer) have geographical entities.
We note that the term 'geography' is also applied to the Earth's moon, Mars, Venus, and possibly even other moons and planets in our own solar system and beyond. Thus, we are attempting to define things generally enough that they could be reused for the geographical entities/features on the Moon, Mars, other planets, exoplanets, other natural satellites (a.k.a moons), asteroids, etc.
geographical entity
A geographical entity that has at least one bona fide boundary.
geographical feature
A geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface.
A site designated by some relative spatial orientation.
François Modave
An arbitrary part of the Earth defined by human-made boundaries and/or natural features such as rivers.
geographical region
body of water
continent
land mass
island
An object aggregate of geographical entities
aggregate of geographical entities
aggregate of geographical features
aggregate of islands
geopolitical organization
geopoli organization
"Although the very meaning of the term is controversial, it involves authoritative decsionmaking in areas that once were part of national legal frameworks, the government, the sovereign state, or the public sector." Karns and Mingst (2004) p. 14.
Katrina Donovan
Examples: private bond-rating agencies such as Moody's Investors Service, International Chamber of Commerce, Worldwide Responsible Apparel Manufacturing Principles, Forest Stewardship
private governance organization
a geopolitical organization that is voluntary and private, whose members are individual persons or organizations that come together to acheive a common purpose.
NGOs are private voluntary organizations whose members are individuals or associations that come together to acheive a common purpose. Some organizations are formed to advocate a particular cause such as human rights, peace, or envirnomental projetion. Others are established to provide services such as disaster relief, humantarian aid in war-torn socieities, or development assistance. ... National level groups are often called interest or pressure groups, and many of them are now linked to counterpart groups in other countries through transnational networks or federations. International NGOs, like IGOs, may draw their members from one region or several regions, and they may have very specific functions or be multi-functional. Karns and Mingst (2004) p. 10f.
Examples: Internaltion Federation of Red Cross and Red Crescent Societies, Oxfam, CARE, Doctors Without Borders, World Wildlife Fund, Transparency International, Human Rights Watch, Amnesty International, and Save the Children.
nongovernmental organization
an intergovernmental organization that has at least three member states, that has activies in at least three states, and that is unified by some formal intergovernmental agreement
"IGOs are organizations whose memebers include at lesat three states, that have activities in several states, and whose members are held together by a formal intergovernmental agreement ... These organizations range in size from three members (North American Free Trade Argreement [NAFTA]) to more than 190 memembers (Universal Postal Union (UPU)]. Memebers may come from primarily one georgraphic regioni (Oragnaization of American States [OAS]) or from all geographic regions (World Bank). although soem IGOs are designed to achieve a single purpose (Organization of Petroleum exporting countries [OPEC]), others have been developed for multiple tasks (United Nations [UN}). ... IGOs are recognized subjects of international law with separate standing fromt heir member states." Karns and Mingst I(2004) p. 7
examples: North American Free Trade Argreement [NAFTA] , Universal Postal Union [UPU], Oragnaization of American States [OAS], World Bank), Organization of Petroleum exporting countries [OPEC] United Nations [UN[, The World Trade Organization [WTO], The World Health Organization [WHO], UNICEF
intergovernmental organization
A governmental organization with a defined territory on which it exercises internal and external sovereignty, a permanent population, a government, and the capacity to enter into relations with other sovereign states.
de facto sovereign state
de facto state
nation state
Per Wikipedia, the word 'nation' does not always refer to soverign states. For example, the "nation of Islam".
sovereign state
An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii). Note: this definition was taken over from "geopolitical organization".
IMPORTANT: The label "geopolitical organization" was previously used for OMRSE_00000044 (governmental organization). "geopoli organization" is a label for a new and different class.
governmental organization
An object aggregate that is not itself a geopolitical organization and whose members are only geopolitical organizations that have some feature in common
aggregate of geopolitical organizations
obsolete aggregate of dependencies
obsolete aggregate of major administrative subdivisions
An aggregate of governmental organizations that is not itself a sovereign state and whose members are only sovereign states that have some feature in common
examples: all the sovereign states in North America, all the sovereign states with a GDP below or exceeding a particular quantity of money, all the sovereign states with a constitutional monarchy, all the sovereign states who belong to the U.N. (which is different than the U.N. itself), etc.
aggregate of sovereign states
geodetic coordinate measurement datum
A measurement of location on the Earth that uses a single number to specify a coordinate in a coordinate system known as a geodetic datum.
Josh Hanna
latitude and longitude are key subtypes
geodetic datum
A coordinate system, and a set of reference points, used to locate places on the Earth (or similar objects).
Wikipedia: https://en.wikipedia.org/wiki/Geodetic_datum Date accessed: 2015-04-13
Every latitude and longitude measurement is with respect to a geodetic datum. Most common ones in use are NAD83 and WGS84.
planar angular measurement unit label
plane angle measurement unit label
A sovereign state whose political sovereignty has been recognized by the United Nations, in accordance with international law.
de jure state
Sovereignty, in the legal sense, is acquired by a state upon receiving recognition by the international community. However, without specifying that this recognition can only be acquired through full membership to the United Nations, a non-arbitrary standard would be difficult, if not impossible, to come by since there are a good many sovereign states whose sovereignty is not explicitly recognized by one or more states. Given that the de facto criteria for sovereignty must be achieved prior to membership to the UN General Assembly and that every member therein is considered to be "international recognized," full membership to the UN is a sufficient criterion for de jure sovereignty. This can be further justified by noting that, in cases where UN member X claims to not recognize the sovereign status of UN member Y, the diplomatic and political behavior of member X towards Y nevertheless tacitly implies that it recognizes Y's sovereignty.
de jure sovereign state
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
This is the same as GO molecular function
gene product or complex activity
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
A biological process is an evolved process
Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
biological process
A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
See also the biological process terms 'viral infectious cycle ; GO:0019058' and 'lysogeny ; GO:0030069'.
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
viral assembly, maturation, egress, and release
The specific behavior of an organism that is associated with reproduction.
reproductive behavior in a multicellular organism
multicellular organism reproductive behavior
A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid).
Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.
A type of reproduction in which new individuals are produced from a single organism, either from an unfertilized egg or from a single cell or group of cells.
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.
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
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.
OBSOLETE. The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
The reason for obsoletion is that this term is equivalent to multicellular organismal reproductive process.
obsolete multicellular organism reproduction
A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts.
symbiosis, encompassing mutualism through parasitism
symbiotic interaction between host and organism
biological process involved in symbiotic interaction
Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
entry into cell of other organism during symbiotic interaction
entry into host cell via penetration peg
entry into host via a specialized structure during symbiotic interaction
entry into host via enzymatic degradation of host anatomical structure
entry into host via enzymatic degradation of host cuticle
penetration into host via a specialized structure
penetration into host via a specialized structure during symbiotic interaction
entry into cell of other organism involved in symbiotic interaction
entry into other organism during symbiotic interaction
entry into other organism involved in symbiotic interaction
Any process evolved to enable an interaction with an organism of a different species.
interspecies interaction between organisms
interspecies interaction with other organisms
biological process involved in interspecies interaction between organisms
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 localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
Gene Ontology: http://purl.obolibrary.org/obo/go.owl
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.
biological process involved in interaction with host
A biological process which involves another organism of the same or different species.
conditional specification
A directive information entity that specifies what should happen if the trigger condition is fulfilled.
PlanAndPlannedProcess Branch
OBI branch derived
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A data item label that denotes a unit of measure.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Melanie Courtot
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
narrative object
Examples of narrative objects are reports, journal articles, and patents submission.
A narrative object is an information content entity that is a set of propositions.
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
person:Chris Stoeckert
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
data item label
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
An information content entity that is part of some data item and is used to partially define the denotation of that data item.
GROUP: IAO
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
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
obsolete_digital entity
A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality'
obsolete2_digital entity
journal article
Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
A report that is published in a journal.
information carrier
In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
A quality of an information bearer that imparts the information content
12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
model number
A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
binary digital entity
MS Word document, ZIP file, DICOM file, JPEG file
A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity'
digital_entity
obsolete2_binary digital entity
a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
programming language
R, Perl, Java
A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
data
symbol
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
PERSON: James A. Overton
based on Oxford English Dictionary
numeral
A symbol that denotes a number.
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
integer numeral
A numeral that denotes an integer
scalar measurement datum
10 feet. 3 ml.
A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
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.
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
directive information entity
time trigger
obsolete_study interpretation
A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses
2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application."
2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead.
Lawrence Hunter
dot plot
Dot plot of SSC-H and FSC-H.
A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
person:Allyson Lister
graph
A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
PERSON: Lawrence Hunter
text based digital entity
XML file, C++ source code file
A text based digital entity is a digital entity that is encoded so that it only contains text characters.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document'
obsolete2_text based digital entity
rule
example to be added
A rule is an executable which guides, defines, restricts actions.
MSI
PRS
contour plot
Contour plot of SSC-H, FSC-H, and FL1-H.
generically_dependent_continuants
group:Flow Cytometry community
report figure
A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report
Replaced by defined version of figure
obsolete2_report figure
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
software interpreter
R program, Perl interpreter, Java virtual machine
A software interpreter is a software application that executes some specified input software.
Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
density plot
Density plot of SSC-H and FSC-H.
A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
report
Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record).
2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.
2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
report element
A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page).
2009-03-16: needs some more work (clarify relations).
2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.
There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text
PERSON: Allyson Lister
obsolete_report element
binary executable
Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
person:Jennifer Fostel
obsolete2_binary executable
source code module
The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
A source code module is a directive information entity that specifies, using a programming language, some algorithm.
report table
A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion
obsolete_report table
data format specification
A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
image
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Clint Dowland
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
digital document
A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'
obsolete2_digital document
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?
_identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.
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
serial number
A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
lot number
A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
batch number
A settings datum is a datum that denotes some configuration of an instrument.
2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.
Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
setting datum
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
Need to rework digital entity. Digital quality was suggested by Barry.
conclusion textual entity
that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
2009/10/23 Alan Ruttenberg: We need to work on the definition still
material information bearer
A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
a brain
a hard drive
A material entity in which a concretization of an information content entity inheres.
histogram
A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
PERSON:Chris Stoeckert
PERSON:James Malone
heatmap
A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
Venn diagram
A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
WEB: http://en.wikipedia.org/wiki/Venn_diagram
obsolete_survival curve
A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
WEB: http://www.graphpad.com/www/book/survive.htm
dendrogram
Dendrograms are often used in computational biology to illustrate the clustering of genes.
A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
WEB: http://en.wikipedia.org/wiki/Dendrogram
scatter plot
Comparison of gene expression values in two samples can be displayed in a scatter plot
A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
scattergraph
WEB: http://en.wikipedia.org/wiki/Scatterplot
A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
PERSON:Joanne Luciano
WEB: http://en.wiktionary.org/wiki/photograph
photograph
photographic print
A photographic print is a material entity upon which a photograph generically depends.
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
textual entity
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
text
citation
Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
A textual entity intended to identify a particular publication.
author identification
L. Hunter
A textual entity intended to identify a particular author
institutional identification
University of Colorado Denver School of Medicine
A textual entity intended to identify a particular institution
caption
Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
A textual entity that describes a figure
document title
Textual characteristics of traditional and Open Access scientific journals are similar
A textual entity that names a document
table
| T F --+----- T | T F F | F F
A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
table of abbreviations
IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
A table where the constituent texts are abbreviations and their expansions
figure
Any picture, diagram or table
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
diagram
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
A figure that expresses one or more propositions
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
publication
journal article, newspaper story, book, etc.
A document that is the output of a publishing process.
PERSON: Jie Zheng
published document
Revisit the term in Octorber 2020. Improve the defintion.
publication about an investigation
Most scientific journal articles
A publication that is about an investigation
scientific publication
patent
US Patent 6,449,603
A document that has been accepted by a patent authority
document part
An abstract, introduction, method or results section.
An information content entity that is part of a document.
abstract
The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.
A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
precis
introduction to a publication about an investigation
Section labelled 'introduction' of a typical scientific journal article
A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
background
introduction
overview
methods section
The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
A part of a publication about an investigation that is about the study design of the investigation
experimental
experimental methods
experimental procedures
experimental section
method
methodology
methods
results section
The section labelled 'results' in a typical scientific journal article
A part of a publication about an investigation that is about a study design execution
results
discussion section of a publication about an investigation
A part of a publication about an investigation that is about the study interpretation of the investigation
discussion
discussion section
discussions
references section
The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
A part of a document that has citations as parts
literature cited
reference
reference list
references
Lawrence Hunter and Kevin Brettonel Cohen
A part of a document that enumerates the authors of the document
institution list
The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
A part of a document that has parts that are institution identifications associated with the authors of the document
author contributions section
LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript.
A part of a publication that is about the specific contributions of each author
author contributions
authors' contribution
authors' contributions
authors' roles
contributions by the authors
contributorship
acknowledgements section
The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
Part of a publication that is about the contributions of people or institutions other than the authors.
acknowledgement
acknowledgements
acknowledgment
acknowledgments
footnote
The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.
A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.
endnote
footnotes
supplementary material to a document
A part of a document that is segregated from the rest of the document due to its size
additional file
additional files
additional information
appendix
electronic supplementary material
electronic supplementary materials
supplemental data
supplemental information
supplemental material
supplementary data
supplementary files
supplementary information
supplementary material
supplementary materials
supporting information
table of contents
A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred).
table of figures
A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred).
running title
A shorter version of a document title
copyright section
This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
A document part that describes legal restrictions on making or distributing copies of the document
A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
AR notes: We need to discuss whether it should include site.
cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
one dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
two dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
three dimensional cartesian spatial coordinate datum
A scalar measurement datum that is the result of measurement of length quality
length measurement datum
denotator type
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Barry Smith, Werner Ceusters
A scalar measurement datum that is the result of measurement of mass quality
mass measurement datum
hypothesis textual entity
A textual entity that expresses an assertion that is intended to be tested.
A scalar measurement datum that is the result of measuring a temporal interval
time measurement datum
A textual entity that is used as directive to deliver something to a person, or organization
2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59
postal address
email address
Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583
Person:Chris Stoeckart
author role
A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
data item extraction from journal article
A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free.
Person: Jie Zheng
VEuPathDB
publishing process
A document that is in preparation for submission to be published.
EFO_0001795 in preparation
document in preparation for publication
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
A planned process in which a document is created or added to by including the specified input in it.
6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
Bjoern Peters
wikipedia http://en.wikipedia.org/wiki/Documenting
documenting
line graph
A line graph is a type of graph created by connecting a series of data points together with a line.
line chart
WEB: http://en.wikipedia.org/wiki/Line_chart
A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
Person:Melanie Courtot
assigning a centrally registered identifier
Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them.
A planned process in which a CRID registry associates an information content entity with a CRID symbol
associating information with a CRID in the CRID registry
associating information with a centrally registered identifier in its registry
a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Bill Hogan
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
centrally registered identifier
PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles.
A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process.
Justin Whorton
centrally registered identifier registry
Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID.
A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
looking up a centrally registered identifier
time stamped measurement datum
pmid:20604925 - time-lapse live cell microscopy
A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
experimental time series
time sampled measurement data set
written name
"Bill Clinton"
"The Eiffel Tower"
"United States of America"
A textual entity that denotes a particular in reality.
The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.
A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
PERSON: Michel Dumontier
software method
A software module is software composed of a collection of software methods.
PERSON: Melanei Courtot
software module
A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
software library
A software application is software that can be directly executed by some processing unit.
software application
A software script is software whose instructions can be executed using a software interpreter.
software script
abbreviation textual entity
From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect.
A textual entity listing abbreviations and their expansions that are used in a document.
PERSON: Bill Baumgartner
abbreviations section
The section labelled 'abbreviations' in a typical scientific journal article.
A part of a document where abbreviations and their long-forms used within the document are listed.
abbreviation and acronyms
abbreviation list
abbreviations
abbreviations and acronyms
abbreviations list
abbreviations used
definitions for abbreviations
list of abbreviations
list of abbreviations used
non-standard abbreviations
nonstandard abbreviations
nonstandard abbreviations and acronyms
author information section
The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/)
A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
author information
authors’ information
biographies
contributor information
author information textual entity
From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD.
A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
author summary section
The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/)
A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers.
author summary
summary
synopsis
Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)
author summary textual entity
From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX.
A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).
availability section
The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained.
availability
availability of data
data archiving
data availability
data availability statement
data sharing statement
availability textual entity
From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): Project home page:http://krux.googlecode.com
A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained.
case report section
The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/)
A part of a document about the medical history of a specific patient as it relates to the topic of the document.
case presentation
case report
case report textual entity
Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension.
A textual entity that expresses a detailed account of a portion of the medical history for a specific patient.
conclusion section
The section labelled 'conclusion' in a typical scientific journal article.
A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document.
concluding remarks
conclusion
conclusions
findings
conflict of interest section
The section labelled 'conflict of interest statement' in a typical scientific journal article.
A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document.
authors' disclosures of potential conflicts of interest
competing financial interests
competing interests
conflict of interest
conflict of interest statement
conflict of interests
conflicts of interest
declaration of competing interest
declaration of competing interests
declaration of interest
declaration of interests
disclosure of conflict of interest
disclosure of potential conflicts of interest
duality of interest
statement of interest
SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)]
A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document.
conflict of interest textual entity
consent section
The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)
A part of a document about the consent process that was used to enroll patients in a study.
consent
consent textual entity
From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal.
A textual entity that documents the consenting process used to enroll patients in a study.
ethical approval section
The section labelled 'ethical approval' in a typical scientific journal article.
A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis.
ethical approval
ethical requirements
ethics
ethics statement
ethical approval textual entity
From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review.
A textual entity that documents the ethical approval of some study design.
figures section
The section labelled 'figures' in a typical scientific journal article.
A part of a document that contains one or more figures.
figures
funding source declaration section
The section labelled 'funding' in a typical scientific journal article.
A part of a document used to detail information regarding the source of funding used in support of the generation of the document content.
financial support
funding
funding information
funding sources
funding statement
funding/support
grants
role of the funding source
source of funding
sources of funding
study funding
funding souce declaration textual entity
From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication.
A textual entity documenting the source of funding that supported some study.
funding source declaration textual entity
future directions section
The section labelled 'future directions' in a typical scientific journal article.
A part of a document detailing extensions of the described work that may be implemented at some future point in time.
future challenges
future considerations
future developments
future directions
future outlook
future perspectives
future plans
future prospects
future research
future research directions
future studies
future work
outlook
future directions textual entity
Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members.
A textual entity expressing ideas regarding future work relevant to work described in a document that could be done.
genome announcement section
The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/)
A document part announcing the publication of a novel draft genome sequence.
genome announcement
genome announcement textual entity
Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB).
A textual entity that describes the generation and public release of a novel, draft genome sequence.
keyword textual entity
From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): Exon orthology; alternative splicing; exon duplication; intron-exon structure.
A textual entity listing keywords indicating the major theme(s) of a document.
keywords section
The section labelled 'keywords' in a typical scientific journal article.
A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed.
keywords
study limitations section
The section labelled 'limitations' in a typical scientific journal article.
A part of a document about biases or short comings related to the study design and execution.
limitations
study limitations
Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
study limitations textual entity
Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out.
A textual entity addressing a shortcoming or bias of a study design or execution.
materials section
The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)
A part of a document about the materials required to reproduce the content of the document.
materials
notes section
The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):
A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc.
notes
patients section
The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/)
A part of a document about the patients that participated in a study.
patients textual entity
Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred.
A textual entity expressing information regarding the patients used in a study.
pre-publication history section
The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/)
A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors.
notice of republication
pre-publication history
pre-publication history textual entity
From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): The pre-publication history for this paper can be accessed here: http://www.biomedcentral.com/1471-2253/13/33/prepub
A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information.
related work section
The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/)
A part of a document about work in other publications that is relevant to the content of the document.
related literature
related work
related work textual entity
Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).
A textual entity that discusses work from other publications and expresses their relevancy to the content of a document.
requirements section
A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource.
requirements
requirements textual entity
From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): • Operating systems: Platform independent • Programming language: Matlab, R, Python • Other requirements: None • License: GNU GPL v3 • Any restrictions to use by non-academics: None
A textual entity that expresses the requirements necessary to use a resource, e.g. software.
statistical analysis textual entity
From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant.
A textual entity documenting statistical analysis tools and techniques employed.
statistical analysis section
The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)
A part of the document used to describe the statistical methodologies employed in the work presented in the document.
statistical analysis
tables section
The section labelled 'tables' in a typical scientific journal article.
A part of a document that contains one or more tables.
tables
An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail.
postal code
A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region.
Postal delivery route
A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes.
ZIP code
zone improvement plan code
database extract, transform, and load process
A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second.
Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second
Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output.
ETL
descriptive data section
A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made.
additional results section
A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.)
research participants section
A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.).
measurement methods section
A methods section that describes details of data assessment methods (data measurement).
research settings section
A document part that describes the physical/social/cultural conditions around a research trial.
study bias section
A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others.
graphical abstract
An abstract that is pictorial summary of the main findings described in the document.
visual abstract
A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistantly identify oneself as a human researcher or contributor.
"You can connect your iD with your professional information — affiliations, grants, publications, peer review, and more. You can use your iD to share your information with other systems, ensuring you get recognition for all your contributions, saving you time and hassle, and reducing the risk of errors." [https://orcid.org/]
This class was originally defined in Apollo_SV (http://purl.obolibrary.org/obo/APOLLO_SV_00000496) but due to it being more in scope of IAO, it was decided to add it to IAO and deprecate its Apollo_SV equivalent. (2022-10-25)
Open Researcher and Contributor Identifier
ORCID identifier
identifier
An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
proper name
Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB)
alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems
An information content entity that is a fundamental unit in a written language.
Grapheme is not about anything and hence is likely to not be an information content entity. If a new subclass of GDC for information structure entities is created it should move there.
grapheme
A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
dubbing process
naming
identifier creating process
A personal name is a proper name identifying an individual person.
An identifier referring to an individual entity that is ascribed personhood by the user of the identifier.
Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name)
Personal names to not include names of fictional characters, e.g. Sherlock Holmes.
Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB)
personal name
A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name
first name
given name
An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children.
last name
surname
family name
An information content entity that is a collection of other information content entities that has been created to identify or annotate core ideas of a specified domain, and where the intention of its creators is that the aggregated entities have a one-to-one correspondence with entities in reality outside the aggregate.
An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things.
code map
code system
codeset
coding system
controlled vocabulary
Code sets might include non-entities/things (e.g. missing thumbs).
Does not imply absence vs. presence of any taxonomy.
Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities.
Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).
For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).
For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.
Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain.
The information content entities do not denote each other.
code set
Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom
A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived.
The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012). Reinach clearly does not imply that a command that does not fulfill its prupose would not be a command. Thanks to W.R. Hogan for finding the Reinach quote.
social act
A social act that creates or revokes a deontic role.
deontic declaration
ontology module
I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
ontology file
This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.
base ontology module
An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.
editors ontology module
An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
source ontology module
main release ontology module
An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module
bridge ontology module
An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.
import ontology module
A subset ontology module that is intended to be imported from another ontology.
TODO: add axioms that indicate this is the output of a module extraction process.
import file
subset ontology module
An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
ontology slim
subset ontology
curation subset ontology module
A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.
analysis ontology module
An ontology module that is intended for usage in analysis or discovery applications.
analysis subset ontology module
single layer ontology module
A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
ribbon subset
single layer subset ontology module
exclusion subset ontology module
A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
antislim
external import ontology module
An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
external import
species subset ontology module
A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
taxon subset
reasoned ontology module
An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.
generated ontology module
An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process
template generated ontology module
An ontology module that is automatically generated from a template specification and fillers for slots in that template.
taxonomic bridge ontology module
ontology module subsetted by expressivity
obo basic subset ontology module
A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports
ontology module subsetted by OWL profile
EL++ ontology module
An infectious disposition to become part of a disorder only in organisms whose defenses are compromised.
opportunitistic pathogenic disposition
The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host.
This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin).
opportunistic infectious disposition
An infectious disposition to become part of a disorder in organisms that have intact defenses.
A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts.
A quote from page 3 of Mandell's "Principles and Practice of Infectious Diseases" (Sixth edition): "It is useful to distinguish "principal" pathogens, which regularly cause disease in some proportion of susceptible individuals with apparently intact defense systems, from other potentially pathogenic microorganisms. ... even for most organisms classified as principal pathogens, for example, Staphylococcus aureus and the pneumococcus, some impairment or local breakdown in normal host defense mechanisms must occur for these bacteria to cause disease. ... Thus, it seems clear that the capacity of certain microorganisms to cause disease in seemingly uncompromised human hosts on a regular basis reflects some fundamental difference in their virulence capabilities from those of opportunists and the more numerous commensal species that rarely, if ever, cause disease."
primary infectious disposition
A disposition to initiate processes that result in a disorder.
pathogenicity
A pathogenic disposition is realized in processes that create a disorder.
The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition. By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition.
pathogenic disposition
A pathogenic disposition that inheres in an organism and is a disposition for that organism (1) to be transmitted to a host, (2) to establish itself in the host, (3) to initiate processes that result in a disorder in the host, and (4) to become part of that disorder.
The disposition is realized in a process that has as part a transmission process, an establishment in host process, a process that results in a disorder, and a process in which the bearer of the disposition becomes part of that disorder. The infectious disposition has a complementary disposition that inheres in an organism and is the capability to be host to an organism with an infectious disposition and to undergo processes initiated by that infectious organism that result in a disorder.
An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host.
An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis.
zoonotic disposition
An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host.
An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis.
reverse zoonotic disposition
An organism that has immunocompetence.
immunocompetent organism
A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process.
The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening.
infectious agent transmissibility
A quality that inheres in an infectious agent and is the liklihood that the infectious disposition will be realized upon exposure of a susceptible organism.
This quality is measured by the proportion of exposed who become infected.
infectivity
A quality that inheres in an infectious agent and is the degree to which realizations of the infectious disease caused by the infectious agent become severe or fatal.
This quality is measured by the proportion of clinically apparent cases that are severe or fatal.
virulence
A quality that inheres in an entity and is the degree to which it can be harmed by another entity.
Low susceptibility is often referred to as resistance. In this sense, resistance is a quality.
A quality that inheres in an organism population and is the number of realizations of an infectious disease for which the infectious disease course begins during a specified period of time.
A particular instance of infectious disease incidence will depend on a type of infectious disease, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure.
infectious disease incidence
A quality that inheres in an organism population and is the number of organisms in the population that become infected with an infectious agent during a specified period of time.
A particular instance of infection incidence will depend on a type of infectious agent, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure.
infection incidence
A quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time and in whom the infectious disease begins during the specified period of time.
cumulative incidence of infectious disease
An instance of infectious disease incidence proportion is measured by dividing a measure of an instance of infectious disease incidence by the number of members of the population in which the infectious disease course had not begun at the beginning of the specified period of time over which the incidence was measured.
infectious disease incidence proportion
A quality that inheres in an organism population and is the proportion of members of the population not infected at the beginning of a specified period of time who become infected during the specified period of time.
cumulative incidence of infection
An instance of infection incidence proportion is measured by dividing a measure of an instance of infection incidence by the number of members of the population not infected at the beginning of the specified period of time over which the incidence was measured.
infection incidence proportion
A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time.
An instance of infectious disease incidence rate is measured by dividing a measure of an instance of the infectious disease incidence proportion by the length of the period of time over which the incidence was measured.
infectious disease incidence rate
A quality that inheres in an organism population and is the infection incidence proportion per unit time.
An instance of infection incidence rate is measured by dividing a measure of an instance of infection incidence proportion by the length of the period of time over which the incidence was measured.
infection incidence rate
A quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time.
Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease prevalence will depend on a type of infectious disease, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics.
infectious disease prevalence
A quality that inheres in an organism population and is the number of organisms in the population infected with an infectious agent at a specified time.
Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infection prevalence will depend on a type of infectious agent, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics.
infection prevalence
A quality that inheres in an organism population and is the number of organisms in the population who have, at any point during their lives, been bearers of an infectious disease and experienced realization of the disease.
Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease lifetime prevalence will depend on a type of infectious disease and a population. Actual measures of prevalence are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics.
infectious disease lifetime prevalence
A quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for an infectious agent in their serum at a specified time.
Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious agent seroprevalence will depend on a type of infectious agent and a population. Actual measures of seroprevalence are based only on tested individuals and usually specify a geographic location. Other constraints may include population demographics.
infectious agent seroprevalence
A quality that inheres in an organism population and is the per capita number of deaths in the population resulting from an infectious disease over a specified period of time.
A particular instance of infectious disease mortality rate will depend on a type of infectious disease and a population. Actual measures of mortality rate are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. Mortality rate is typically expressed in units of deaths per 1000 individuals per year.
infectious disease mortality rate
A quality that inheres in an organism population in virtue of the fact that infections of the type that causes an infectious disease are maintained in the population via intra-population transmission or by transmission from a local reservoir.
A particular instance of infectious disease endemicity will depend on a type of infectious agent and a population. The population may be specified by temporal, geographic, or demographic constraints. Infectious diseases that are typical or common to a particular population are referred to as endemic.
infectious disease endemicity
A quality that inheres in an organism population by virtue of the fact that realizations of an infectious disease occur in the population with a fluctuating prevalence.
Sporadic quality of infectious disease is relational to previous prevalence of the disease.
infectious disease sporadicity
An aggregate of organisms of the same Species.
The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age.
organism population
A material entity with a pathogenic disposition.
An infectious agent with a primary infectious disposition.
primary pathogen
An organism bearing a host role.
An organism that has an infectious disposition.
infectious agent
A process that attenuates an immune response.
immunosuppression
A disposition that is the ability to mount a normal immune response.
The disposition inheres in a bearer in virtue of the fact that the bearer has all canonical immune system components and none are disordered. The disposition is realized in a successful immune response.
immunocompetence
An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission.
The disposition is realized in a direct, horizontal transmission process between members of the same Species.
communicability
An establishment of localization process in which a material entity reaches a site in an organism in which it can survive, grow, multiply, or mature.
Requested addition of this term to the GO.
An organism begins bearing a particular host role as soon as the extended organism contains the relevant material entity, regardless of that entity's location in the extended organism. An establishment process is any process by which the entity reaches a location in the extended organism in which it can persist and continue its lifecycle. For example, an organism is host to a virus as soon as any part of the extended organism is occupied by virus particles. During an establishment process, virus particles enter host cells of the relevant type, and viral DNA is integrated into host DNA.
establishment of localization in host
A process by which a disorder comes into existence.
appearance of disorder
A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism.
host role
An infectious agent with an opportunistic infectious disposition.
A pathogen transmission process in which a pathogen is transmitted from one host to another of the same Species, and the two hosts are not in a parent-child relationship.
horizontal pathogen transmission process
Intentionality is the fundamental quality of conscious mental processes of always having content, of being directed towards, or about something.
intentionality
A bodily quality is a quality that inheres in some extended organism.
bodily quality
A mental quality is a bodily quality that inheres in those structures of the extended organism that are essential for mental functioning.
mental quality
"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 <class>
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
Actinobacteria <phylum>
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
Homo sapiens
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 process that realizes a plan which is the concretization of a plan specification.
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
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.
investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
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
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 entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
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
a planned process that carries out a study design
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.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A device is a processed material which is designed to perform some function or functions
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
food should not classify as a device - counter example for using manufacturer and not device. macroscopic only
if we keep this exploratory term we could reinstate the old device class which is obsolete_device. didn't work before as we had manufacturing as part of the definition. device was needed, but couldn't define in Philadelphia. If we decide that in addition to function there are also capabilities for which a device is created we will include these in the definition.
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
latitude coordinate measurement datum
A measurement datum that is the measure of the latitude coordinate of a site.
latitude
longitude coordinate measurement datum
A measurement datum that is the measure of the longitude coordinate of a site.
longitude
Specimen Collection Location - Longitude
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
A value specification that consists of two parts: a numeral and a unit label
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
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/
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
WEB: http://en.wikipedia.org/wiki/Organism
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A data transformation is a process which produces output data from input data
A planned process that produces output data from input data.
Elisabetta Manduchi
Helen Parkinson
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.
A process in which at least one bodily component of an organsim participates.
From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060
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.
From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087
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 health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night.
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 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 role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.
patient
CAFE domain expert working group.
In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications.
patient role
A role that inheres in an organization and that is realized by the providing of services in a health care encounter.
health care provider organization role
An object aggregate of objectual organisms.
Any arbitrary collection of organisms. They need not be of the same taxonomic class.
aggregate of objectual organisms
An object aggregate all of whose components are human beings.
collection of humans
A role in human social processes that inheres in an organization.
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, if realized, is realized by either a health care process or an ancillary health care process
Previous definition: An organization social role played by an organization in health care processes.
organization health care role
A patient role that inheres in a human being.
human patient role
An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common
William R. Hogan Amanda Hicks
It is often convenient to group organizations together that otherwise might not even interact with one another.
aggregate of organizations
material entity role
organism role
Homo sapiens role
organization role
A function inhering in a material entity that, if realized, is realized by that material entity being the site at which formal education is provided to a student population.
school function
A healthcare provider role that inheres in an organization and is realized by providing inpatient 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, if realized, 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 school organization and is the bearer of a school function.
school facility
secondary school role
A human social role that is created by a deontic declaration performed by an organization.
human organizational role
human role within an organization
An information content entity that is about human travel.
human traveling information
health care function
A role that inheres in some entity that is realized in a social act.
Previous definition: A role played by an entity in human social processes.
role in human social processes
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
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 physical magnitude.
A 1-D extent quality which is equal to the distance between two points.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
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 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent.
MIREOT'd into GEO to represent the area quality of a geographical region, including land area and water area.
A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions.
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
A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host.
Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species.
Suggested label: pathogen transmission process
Transmission Ontology: http://purl.obolibrary.org/obo/trans.owl
Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome.
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
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.
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
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 the amount of a 2-dimensional flat surface.
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
supranational entity
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
obsolete_class
organism population universal
atmosphere of the Earth
angular degree
radian
A unit of measurement of planar angles where a full circle is 2π. Specifically the angle is the length of the arc subtended by the angle divided by the circumference of the circle.
Technically in the S.I. system it is a derived unit m•m^-1.
rad
square mile
An area unit which is equal to the area enclosed by a square in a flat plane which is one mile on every side.
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
core
obsolete_core
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
We expect to be able to mine these new reasons and add instances as required.
obsolete_other
universal
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
"A time unit which is equal to 7 days." [Wikipedia:Wikipedia]
"An area unit which is equal to an area enclosed by a square with sides each 1 meter long." [NIST:NIST]
## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation
axiom holds for all times
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).