VICK is an application graph to describe vaccine immunization information. VICK is built on OMRSE and VICO, and based on metadata from Texas immunization records for patients
Vaccine Information and Consent Knowledge base (VICK)
BFO OWL specification label
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 CLIF specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
editor preferred term
editor preferred term~editor preferred label
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
example
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
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.
definition editor
term editor
Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
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 http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
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
term_mapping_to_UMLS
term_mapping_to_NCIT
term_mapping_to_HL7v3
has_MedDRA_id
ISA alternative term
An alternative term used by the ISA tools project (http://isa-tools.org).
ISA tools project (http://isa-tools.org)
The NCBITaxon ontology ID of an organism.
organism NCBITaxon ID
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.
CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
A synonym type for describing abbreviations or initalisms
A synonym type for describing ambiguous synonyms
A synonym type for describing dubious synonyms
EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
A synonym type for describing layperson or colloquial synonyms
CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
A synonym type for describing pluralization synonyms
CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
A synonym type for describing UK spelling variants
A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway
MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.
A synonym type for names that have been used as primary labels in the past.
The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College
A synonym type for the legal entity name
CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label
The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese.
nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis
A synonym type for describing Latin term synonyms.
NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced.
A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.
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.
The PUMS serial number assigned to a housing unit, which is only unique within each state, and which explicitly links the housing unit record with person records in PUMS data.
U.S. Census PUMS serial number
William R. Hogan
ISO 639-1 assigns two-character identifiers to individual human languages. This annotation property is for use in annotating OWL2 individuals in OMRSE that represent languages with their appropriate ISO 639-1 code that designates them in that standard system.
ISO 639-1 code
ISO 639-2/B code
ISO 639-2/B assigns three-character identifiers to individual human languages. This annotation property is for use in annotating OWL2 individuals in OMRSE that represent languages with their appropriate ISO 639-2/B ('B' is for "bibliographic applications") code that designates them in that standard system.
ISO 639-2/T code
ISO 639-2/T assigns three-character identifiers to individual human languages. This annotation property is for use in annotating OWL2 individuals in OMRSE that represent languages with their appropriate ISO 639-2/T ('T' is for "terminology applications") code that designates them in that standard system.
ISO 639-3 code
ISO 639-3 assigns three-character identifiers to individual human languages. This annotation property is for use in annotating OWL2 individuals in OMRSE that represent languages with their appropriate ISO 639-3 code that designates them in that standard system.
A description of an OOSTT class that is aimed at the OOSTT user community and not meant to be definition for use in ontology development, curation or maintenance.
Mathias Brochhausen
OOSTT user-centered description
temporal interpretation
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.
An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.
logical macro assertion
A logical macro assertion whose domain is an IRI for a property
logical macro assertion on a property
logical macro assertion on an object property
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
A metadata relation between a class and its taxonomic rank (eg species, family)
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
disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string
An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.
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
is part of
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 as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell.
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
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
b inheres_in c at t =Def. b is a dependent continuant & c is an independent continuant that is not a spatial region & b s-depends_on c at t. (axiom label in BFO2 Reference: [051-002])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'inheres in at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'inheres in@en(x,y,t)'.
BFO 2 Reference: Inherence is a subrelation of s-depends_on which holds between a dependent continuant and an independent continuant that is not a spatial region. Since dependent continuants cannot migrate from one independent continuant bearer to another, it follows that if b s-depends_on independent continuant c at some time, then b s-depends_on c at all times at which a exists. Inherence is in this sense redundantly time-indexed.For example, consider the particular instance of openness inhering in my mouth at t as I prepare to take a bite out of a donut, followed by a closedness at t+1 when I bite the donut and start chewing. The openness instance is then shortlived, and to say that it s-depends_on my mouth at all times at which this openness exists, means: at all times during this short life. Every time you make a fist, you make a new (instance of the universal) fist. (Every time your hand has the fist-shaped quality, there is created a new instance of the universal fist-shaped quality.)
BFO2 Reference: independent continuant that is not a spatial region
BFO2 Reference: specifically dependent continuant
(iff (inheresInAt a b t) (and (DependentContinuant a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [051-002]
inheres in at all times
b bearer_of c at t =Def. c s-depends_on b at t & b is an independent continuant that is not a spatial region. (axiom label in BFO2 Reference: [053-004])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'bearer of at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'bearer of@en'(x,y,t)
(iff (bearerOfAt a b t) (and (specificallyDependsOnAt b a t) (IndependentContinuant a) (not (SpatialRegion a)) (existsAt b t))) // axiom label in BFO2 CLIF: [053-004]
bearer of at some time
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
is 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])
if a realizable entity b is realized in a process p, then p stands in the has_participant relation to the bearer of b. (axiom label in BFO2 Reference: [106-002])
(forall (x y z t) (if (and (RealizableEntity x) (Process y) (realizesAt y x t) (bearerOfAt z x t)) (hasParticipantAt y z t))) // axiom label in BFO2 CLIF: [106-002]
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
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
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])
(forall (x y t) (if (realizesAt x y t) (and (Process x) (or (Disposition y) (Role y)) (exists (z) (and (MaterialEntity z) (hasParticipantAt x z t) (bearerOfAt z y t)))))) // axiom label in BFO2 CLIF: [059-003]
[copied from inverse property 'has participant 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 'has participant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has participant@en'(x,y,t)
[copied from inverse property 'has participant at some time'] BFO 2 Reference: Spatial regions do not participate in processes.
[copied from inverse property 'has participant at some time'] BFO2 Reference: independent continuant that is not a spatial region, specifically dependent continuant, generically dependent continuant
[copied from inverse property 'has participant at some time'] BFO2 Reference: process
participates_in
[copied from inverse property 'has participant at some time'] has_participant is an instance-level relation between a process, a continuant, and a temporal region at which the continuant participates in some way in the process. (axiom label in BFO2 Reference: [086-003])
participates in
participates in 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 'has participant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has participant@en'(x,y,t)
BFO 2 Reference: Spatial regions do not participate in processes.
BFO2 Reference: independent continuant that is not a spatial region, specifically dependent continuant, generically dependent continuant
has_participant
has_participant is an instance-level relation between a process, a continuant, and a temporal region at which the continuant participates in some way in the process. (axiom label in BFO2 Reference: [086-003])
if b has_participant c at t & c is a generically dependent continuant, then there is some independent continuant that is not a spatial region d, and which is such that c g-depends on d at t & b s-depends_on d at t. (axiom label in BFO2 Reference: [091-003])
if b has_participant c at t & c is a specifically dependent continuant, then there is some independent continuant that is not a spatial region d, c s-depends_on d at t & b s-depends_on d at t. (axiom label in BFO2 Reference: [090-003])
if b has_participant c at t then b is an occurrent. (axiom label in BFO2 Reference: [087-001])
if b has_participant c at t then c exists at t. (axiom label in BFO2 Reference: [089-001])
if b has_participant c at t then c is a continuant. (axiom label in BFO2 Reference: [088-001])
(forall (x y t) (if (and (hasParticipantAt x y t) (GenericallyDependentContinuant y)) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (genericallyDependsOn y z t) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [091-003]
(forall (x y t) (if (and (hasParticipantAt x y t) (SpecificallyDependentContinuant y)) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t) (specificallyDependsOnAt y z t))))) // axiom label in BFO2 CLIF: [090-003]
(forall (x y t) (if (hasParticipantAt x y t) (Continuant y))) // axiom label in BFO2 CLIF: [088-001]
(forall (x y t) (if (hasParticipantAt x y t) (Occurrent x))) // axiom label in BFO2 CLIF: [087-001]
(forall (x y t) (if (hasParticipantAt x y t) (existsAt y t))) // axiom label in BFO2 CLIF: [089-001]
has participant
has participant at some time
[copied from inverse property 'concretizes at some time'] You may concretize a piece of software by installing it in your computer
[copied from inverse property 'concretizes at some time'] You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head.
[copied from inverse property 'concretizes at some time'] you may concretize a poem as a pattern of memory traces in your head
[copied from inverse property 'concretizes 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 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t)
[copied from inverse property 'concretizes at some time'] b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002])
concretized by at some time
You may concretize a piece of software by installing it in your computer
You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head.
you may concretize a poem as a pattern of memory traces in your head
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t)
b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002])
if b g-depends on c at some time t, then there is some d, such that d concretizes b at t and d s-depends_on c at t. (axiom label in BFO2 Reference: [076-001])
(forall (x y t) (if (concretizesAt x y t) (and (SpecificallyDependentContinuant x) (GenericallyDependentContinuant y) (exists (z) (and (IndependentContinuant z) (specificallyDependsOnAt x z t) (genericallyDependsOnAt y z t)))))) // axiom label in BFO2 CLIF: [075-002]
(forall (x y t) (if (genericallyDependsOnAt x y t) (exists (z) (and (concretizesAt z x t) (specificallyDependsOnAt z y t))))) // axiom label in BFO2 CLIF: [076-001]
concretizes at some time
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
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
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
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 all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and '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 all times
Mary located_in Salzburg
the Empire State Building located_in New York.
this portion of cocaine located_in this portion of blood
this stem cell located_in this portion of bone marrow
your arm located_in your body
b located_in c at t = Def. b and c are independent continuants, and the region at which b is located at t is a (proper or improper) continuant_part_of the region at which c is located at t. (axiom label in BFO2 Reference: [045-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'located in at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'located in@en(x,y,t)'.
Located_in is transitive. (axiom label in BFO2 Reference: [046-001])
for all independent continuants b, c, and d: if b continuant_part_of c at t & c located_in d at t, then b located_in d at t. (axiom label in BFO2 Reference: [048-001])
for all independent continuants b, c, and d: if b located_in c at t & c continuant_part_of d at t, then b located_in d at t. (axiom label in BFO2 Reference: [049-001])
(forall (x y z t) (if (and (IndependentContinuant x) (IndependentContinuant y) (IndependentContinuant z) (continuantPartOfAt x y t) (locatedInAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [048-001]
(forall (x y z t) (if (and (IndependentContinuant x) (IndependentContinuant y) (IndependentContinuant z) (locatedInAt x y t) (continuantPartOfAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [049-001]
(forall (x y z t) (if (and (locatedInAt x y t) (locatedInAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [046-001]
(iff (locatedInAt a b t) (and (IndependentContinuant a) (IndependentContinuant b) (exists (r_1 r_2) (and (occupiesSpatialRegionAt a r_1 t) (occupiesSpatialRegionAt b r_2 t) (continuantPartOfAt r_1 r_2 t))))) // axiom label in BFO2 CLIF: [045-001]
located in 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 '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
a has_function b at t =Def. b function_of a at t. (axiom label in BFO2 Reference: [070-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has function at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has function@en'(x,y,t)
(iff (hasFunctionAt a b t) (functionOf b a t)) // axiom label in BFO2 CLIF: [070-001]
has function at some time
has quality at some time
a has_role b at t =Def. b role_of a at t. (axiom label in BFO2 Reference: [068-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has role at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has role@en'(x,y,t)
(iff (hasRoleAt a b t) (roleOfAt b a t)) // axiom label in BFO2 CLIF: [068-001]
has role at some time
b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
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
[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
[copied from inverse property 'located in at some time'] Mary located_in Salzburg
[copied from inverse property 'located in at some time'] the Empire State Building located_in New York.
[copied from inverse property 'located in at some time'] this portion of cocaine located_in this portion of blood
[copied from inverse property 'located in at some time'] this stem cell located_in this portion of bone marrow
[copied from inverse property 'located in at some time'] your arm located_in your body
[copied from inverse property 'located in at some time'] b located_in c at t = Def. b and c are independent continuants, and the region at which b is located at t is a (proper or improper) continuant_part_of the region at which c is located at t. (axiom label in BFO2 Reference: [045-001])
[copied from inverse property 'located in 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 'located in at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'located in@en'(x,y,t)
[copied from inverse property 'located in at some time'] BFO2 Reference: independent continuant
has location at some time
[copied from inverse property 'specifically depends on at some time'] A pain s-depends_on the organism that is experiencing the pain
[copied from inverse property 'specifically depends on at some time'] a gait s-depends_on the walking object. (All at some specific time.)
[copied from inverse property 'specifically depends on at some time'] a shape s-depends_on the shaped object
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
[copied from inverse property 'specifically depends on at some time'] 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
[copied from inverse property 'specifically depends on at some time'] 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
[copied from inverse property 'specifically depends on at some time'] 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
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
[copied from inverse property 'specifically depends on at some time'] 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
[copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
[copied from inverse property 'specifically depends on at some time'] 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
[copied from inverse property 'specifically depends on at some time'] 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
[copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
[copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
[copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
[copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
[copied from inverse property 'specifically depends on at some time'] the two-sided reciprocal s-dependence of the roles of husband and wife [20
[copied from inverse property 'specifically depends on 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 '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)
[copied from inverse property 'specifically depends on at some time'] 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
[copied from inverse property 'specifically depends on at some time'] 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
[copied from inverse property 'specifically depends on at some time'] 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.
[copied from inverse property 'specifically depends on at some time'] BFO2 Reference: specifically dependent continuant\; process; process boundary
[copied from inverse property 'specifically depends on at some time'] 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
has specific dependent at some time
[copied from inverse property 'occupies spatiotemporal region'] BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
[copied from inverse property 'occupies spatiotemporal region'] p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])
has spatiotemporal occupant
BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])
occupies spatiotemporal region
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
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
projects onto spatial region at some time
spatial projection of spatiotemporal at some time
projects onto temporal region
temporal projection of spatiotemporal
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
[copied from inverse property 'exists at'] BFO2 Reference: entity
[copied from inverse property 'exists at'] BFO2 Reference: temporal region
[copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
during which exists
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'bearer of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'bearer of@en(x,y,t)'.
bearer of at all times
has quality 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 'has role at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has role@en(x,y,t)'.
has role 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 'has participant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has participant@en(x,y,t)'.
has participant at all times
has specific dependent 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 '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)
specifically depends on 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 'located in at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'located in@en'(x,y,t)
located in 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 some time'] 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 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & '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 some time'] 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 some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t)
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 some time
[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)'.
[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'
part of continuant at all times
[copied from inverse property 'part of continuant at some time'] 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 some time'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
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 some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t)
[copied from inverse property 'part of continuant 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 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t)
[copied from inverse property 'part of continuant at some time'] 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 some time'] 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 some time'] BFO2 Reference: continuant
[copied from inverse property 'part of continuant at some time'] 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 some time'] 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 some time
[copied from inverse property 'has continuant part at all times'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(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 'has continuant part at all times'
[copied from inverse property 'has continuant part 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 '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)'.
part of continuant at all times that whole exists
[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
has measurement unit label
The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend
c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense
see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
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.
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
a relation that links an informed consent form to an associated IRB number
is associated with review board approval number
an object perperty that represents a relation between a unique identifier (ID) and an organization that assigns the ID.
has participant quality
adverse event occurs 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.
Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.
owns
a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b.
is owned by
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
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
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
is_manufactured_by
http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
Liju Fan
has_make
has_manufacturer
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.
is specified output 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
This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
has organization member
Relating an organization to a legal person or organization.
See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
a 'part of continuant at some time' relation that incides a genome belongs to a organism.
is genome of organism
a relation between a gene and the organism where this gene belongs to the organism in nature. It does not include a foreign gene that is transferred to an organism by a genetic engineering method.
is gene of organism
Reinach, A. S�mtliche Werke. Texkritische Ausgabe, M�nchen: Philosophia Verlag, 1989, p.189-204.
BFO relation takes precedence.
We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation.
At the instance level, this relation is the named inverse of is-aggregate-of. At the type level, however, not so. We expect BFO 2.0 to have this relation as well, and we will obsolete this property and declare it equivalent to BFO's version when BFO 2.0 comes out.
is administered by
is enrolled in school
is admitted to hospital
provides service
Relation between an abusive behavior and one upon whom it is inflicted.
Matthew Diller
S. Clint Dowland
is abuse of
Relation between an abusive behavior and one who inflicts it upon someone or something else.
has aggressor
A relation between a household and a material entity that the household stores their possessions in and sleeps in habitually.
lives in
Relation in which a categorization scheme stands to each category into which it partitions things.
demarcates
Relation in which a category stands to the categorization scheme that demarcates it as a category.
demarcated by
Relation in which a data item stands to the person it is both about and primarily associated with.
has primary data subject
The inverse of has primary data subject.
primary data subject of
Relation in which a personal data disclosure stands to the person who performs it by disclosing data items about someone.
has reporter
The inverse of has reporter.
reporter of
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
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
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.
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 or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes.
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.
is concretized as
concretizes
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.
A relationship between a specifically dependent continuant or process 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 or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes 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
has role
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
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/
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
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
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 part of relation that applies only between occurrents.
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.
Primitive instance level timing relation between events
before or simultaneous with
t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
before
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)
immediately preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
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
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.
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.
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
OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role
Obsoleted as the inverse property was obsoleted.
OBSOLETE x has participant y if and only if x realizes some active role that inheres in y
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.
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
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.
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 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.
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
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
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 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 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.
a relation between a question or a questionnaire that is specifically designed for a certain vaccination procedure.
It is not clear if all questionnaires use the same question for a certain vaccination. If it is true, this relation is class level relation. If not, it is instance level relation. However, in a questionnaire and vaccination procedure, this is always true.
is about vaccination procedure
asking vaccination patient
an object property that represents a relation between a document and an entity that writes, maintains and releases the document.
documented by
screening questionnaire is filled by
used in geographic location
has gender
has_vaccine_contraindication is a relation that specifies contraindication of a vaccine.
This relation may be replaced by has_vaccine_allergen. We need to determine if any vaccine contraindicator is not a vaccine allergen.
a object property that specifies a relation between a vaccine and a vaccine allergen
an object property that specifies a relation between a vaccine and a vaccinate route
is_distributed_by is a relation that specifies a company that distributes a product (e.g., vaccine). The company is very likely not the manufacturer of the product.
vaccine immunization against disase
A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in
A relation between a dependent continuant D and an entity E. D inheres_in E iff: given any d that instantiates D at t, there exists some e that instantiates E at t and d *inheres_in* e at t. Here *inheres_in* is the primitive instance level relation.
inheres_in_part_of
A relation between a role R and an entity E. R role_of E iff: R inheres_in E and R is a role
P unfolds_in C : the execution of P is spatially contained by C. forall pP, forall c' partipates_in p, c' located_in C at t, for some t in P
is reported by
has vaccine adverse signs
has symptoms
is documented by
placed on
has measurement value
has x coordinate value
has z coordinate value
has y coordinate value
The only valid string values for this property are ISO 8601 formatted date strings in extended form. It is allowable specify only the year, e.g. '2016' but only when the 1D temporal region references the entire year. Ditto for month, e.g. 2016-04 is acceptable but only if it references the entire interval of that month.
date
time
time of day
hasAge
has vaccination schedule value
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
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
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
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
A geographical migration of an organism belonging to the species Homo sapiens.
human travel
creating a data set
A planned process that has a data set as its specified output.
data set creation
dataset creation
dataset creating
entity
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])
continuant
a heart
a person
a symphony orchestra
the color of a tomato
the disposition of blood to coagulate
the lawn and atmosphere in front of our building
the mass of a cloud
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
endurant
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]
occurrent
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]
independent continuant
a chair
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])
substantial entity
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]
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
process
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]
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 endocitosis and exocitosis
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 [89
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
realizable entity
the disposition of metal to conduct electricity
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of the reproductive organs
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.
If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
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]
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 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
specifically dependent continuant
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 fish to decay
the disposition of this fish to decay
the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
the function of this heart: to pump blood
the liquidity of 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 mozzarella
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.
mode
property
trope
(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]
role
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 biological grandfather as legal guardian in the context of a system of laws
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 chemical compound in an experiment
the role of a patient relative as defined by a hospital administrative form
the role of a person as a surgeon
the role of a stone in marking a property boundary
the role of a student in a university
the role of a woman as a legal mother in the context of system of laws
the role of ingested matter in digestion
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]
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 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
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]
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
generically dependent continuant
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.
a certain PDF file that exists in different and in several hard drives
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]
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
material entity
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.
Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
Examples: collection of random bacteria, a chair, dorsal surface of the body
Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
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]
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. (axiom label in BFO2 Reference: [138-001])
history
gross anatomical part
Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells.
A carbonyl group with two C-bound amine groups.
A amino cyclitol glycoside that consists of streptidine having a disaccharyl moiety attached at the 4-position. The parent of the streptomycin class
2,4-Diguanidino-3,5,6-trihydroxycyclohexyl 5-deoxy-2-O-(2-deoxy-2-methylamino-alpha-L-glucopyranosyl)-3-C-formyl-beta-L-lyxopentanofuranoside
A disaccharide, found most notably in milk, that consists of D-galactose and D-glucose fragments bonded through a beta-1->4 glycosidic linkage. The glucose fragment can be in either the alpha- or beta-pyranose form, whereas the galactose fragment can only have the beta-pyranose form.
Any of a group of aminoglycoside antibiotics produced by fermentation of some Micromonospora spp.
4,6-diamino-3-[3-deoxy-4-C-methyl-3-(methylamino)pentopyranosyloxy]-2-hydroxycyclohexyl 2-amino-2,3,4,6,7-pentadeoxy-6-(methylamino)heptopyranoside
Sucrose is a disaccharide formed by glucose and fructose units joined by an acetal oxygen bridge from hemiacetal of glucose to the hemiketal of the fructose.
beta-D-fructofuranosyl alpha-D-glucopyranoside
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
A dipeptide that has formula C14H18N2O5.
methyl L-alpha-aspartyl-L-phenylalaninate
1-methyl N-L-alpha-aspartyl-L-phenylalanate
3-Amino-N-(alpha-carboxyphenethyl)succinamic acid N-methyl ester
3-Amino-N-(alpha-methoxycarbonylphenethyl) succinamic acid
A (1->6)-alpha-D-glucan which has extra branching consisting of (1->2), (1->3) or (1->4) linkages.
An organic sodium salt that is the monosodium salt of glutamic acid.
A broad-spectrum highly toxic antibiotic or mixture of antibiotics produced by a streptomyces (Streptomyces fradiae) and used medically especially to treat local infections.
An organomercury compound (approximately 49% mercury by weight) used as an antiseptic and antifungal agent.
sodium [(2-carboxylatophenyl)sulfanyl](ethyl)mercurate(1-)
sodium ethyl[2-(sulfanyl-kappaS)benzoato(2-)]mercurate(1-)
[(o-carboxyphenyl)thio]ethylmercury sodium salt
ethyl(2-mercaptobenzoato-S)mercury sodium salt
o-(ethylmercurithio)benzoic acid sodium salt
A heart disease and a myopathy that is characterized by deterioration of the function of the heart muscle.
MSH:D009202 added from NeuroDevNet [WAK].
A hematologic cancer that affects lymphocytes that reside in the lymphatic system and in blood-forming organs.
A cardiovascular system disease that involves the heart.
An immune system disease that is an exaggerated immune response to allergens, such as insect venom, dust mites, pollen, pet dander, drugs or some foods.
hypersensitivity reaction type I disease
A cancer that affects the blood or bone marrow characterized by an abnormal proliferation of blood cells.
An autoimmune disease of peripheral nervous system that causes body's immune system to attack part of the peripheral nervous system.
acute infective polyneuritis NOS (disorder)
A gastrointestinal system disease described as the condition of having frequent loose or liquid bowel movements. Acute diarrhea is a common cause of death in developing countries and the second most common cause of infant deaths worldwide. The loss of fluids through diarrhea can cause severe dehydration which is one cause of death in diarrhea sufferers. Along with water, sufferers also lose dangerous amounts of important salts, electrolytes, and other nutrients. There are at least four types of diarrhea: secretory diarrhea, osmotic diarrhea, motility-related diarrhea, and inflammatory diarrhea.
A blood platelet disease characterized by low a platelet count in the blood.
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
Transient cerebral ischemia (disorder) [Ambiguous]
A hematopoietic system disease that is characterized by a decrease in the normal number of red blood cells.
A B cell deficiency that is caused by a reduction in all types of gamma globulins.
A skin disease characterized by itchy, erythematous, vesicular, weeping and crusting patches of skin.
A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors. The disease has_symptom recurring periods of wheezing (a whistling sound while breathing), has_symptom chest tightness, has_symptom shortness of breath, has_symptom mucus production and has_symptom coughing. The symptoms appear due to a variety of triggers such as allergens, irritants, respiratory infections, weather changes, exercise, stress, reflux disease, medications, foods and emotional anxiety.
chronic obstructive asthma with acute exacerbation
chronic obstructive asthma with status asthmaticus
A hypersensitivity reaction type I disease that is an abnormal response to a food, triggered by the body's immune system.
A thymus cancer that derives_from epithelial cells located_in the thymus. The tumor cells in a thymoma look similar to the normal cells of the thymus, grow slowly, and rarely spread beyond the thymus.
A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
An immune system disease that is an overactive immune response of the body against substances and tissues normally present in the body resulting from an abnormal functioning of the immune system that results in the production of antibodies or T cell directed against the host tissues.
hypersensitivity reaction type II disease
A food allergy that is an allergy or hypersensitivity to dietary substances from the yolk or whites of eggs, causing an overreaction of the immune system which may lead to severe physical symptoms.
A urinary system disease that is located_in the kidney.
A coronary artery disease characterized by myocardial cell death (myocardial necrosis) due to prolonged ischaemia.
A heart disease that is characterized by any structural or functional cardiac disorder that impairs the ability of the heart to fill with or pump a sufficient amount of blood throughout the body.
A Human immunodeficiency virus infectious disease that results_in reduction in the numbers of CD4-bearing helper T cells below 200 per µL of blood or 14% of all lymphocytes thereby rendering the subject highly vulnerable to life-threatening infections and cancers, has_material_basis_in Human immunodeficiency virus 1 or has_material_basis_in Human immunodeficiency virus 2, which are transmitted_by sexual contact, transmitted_by transfer of blood, semen, vaginal fluid, pre-ejaculate, or breast milk, transmitted_by congenital method, and transmitted_by contaminated needles. Opportunistic infections are common in people with AIDS.
A sebaceous gland disease characterized by areas of blackheads, whiteheads, pimples, greasy skin, and possibly scarring.
An artery disease that is characterized by dysfunction of the blood vessels supplying the brain.
A bone inflammation disease that results_in inflammation in the joints of the spine and pelvis. The disease has_symptom pain, has_symptom stiffness in the spine, has_symptom stiffness in the neck, has_symptom stiffness in the hips, has_symptom stiffness in the jaw and has_symptom stiffness in the rib cage.
An arthritis that is an autoimmune disease which attacks healthy cells and tissue located_in joint.
A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide.
Updating out dated CUI and removing lung abscess as a synonym.
A pyoderma consisting of three forms of skin lesions having either a thick, adherent, recurrent, dirty yellow crust with an erythematous margin (common or superficial impetigo) or lessions which are superficial, thin-walled, and bullous as found in bullous impetigo. The lesions in bullous (staphylococcal) impetigo, which are always caused by S aureus, are superficial, thin-walled, and bullous.
A viral infectious disease that results_in infection located_in nerve fiber, has_material_basis_in Human herpesvirus 3, which reactivates after appearing as chickenpox in childhood. The virus is transmitted_by direct contact with the rash, which can develop into chickenpox in newly-infected individuals. The infection has_symptom rash which is followed by blisters, has_symptom headache, has_symptom fever, has_symptom malaise, has_symptom itching, has_symptom burning pain, and has_symptom paresthesia.
A viral infectious disease that results_in infection located_in skin, has_material_basis_in Human herpesvirus 3, which is transmitted_by direct contact with secretions from the rash, or transmitted_by droplet spread of respiratory secretions. The infection has_symptom anorexia, has_symptom myalgia, has_symptom nausea, has_symptom fever, has_symptom headache, has_symptom sore throat, and has_symptom blisters.
An intestinal disease that involves inflammation located_in intestine.
regional enteritis of small intestine with large intestine
MSH:C536215 added from NeuroDevNet [WAK].
(Angina: [crescendo] or [unstable] or [at rest]) or (preinfarction syndrome) or (impending infarction)
A lupus erythematosus that is an inflammation of connective tissue marked by skin rashes, joint pain and swelling, inflammation of the kidneys and inflammation of the tissue surrounding the heart.
A glucose metabolism disease characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.
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".
Amanda Hicks
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
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.
This is the same as GO molecular function
Note that, in addition to forming the root of the molecular function ontology, this term is recommended 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.
gene product or complex activity
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.
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.
biological process
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.
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 measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
purpose of a study; support of hypothesis, discovery of new information
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
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
action specification
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
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
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.
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
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"
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://code.google.com/p/information-artifact-ontology/issues/detail?id=154).
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
10 feet. 3 ml.
A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
scalar measurement datum
directive information entity
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
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.
Philippe Rocca-Serra
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 that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
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.
2009/10/23 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
author list
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
documenting
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
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 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.
dubbing process
naming
identifier creating process
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 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
A document that denotes some identity and is concretized by the bearer of some credential role.
identity document
A documented identity is the aggregate of all data items about an entity. Notice that a documented identity is not itself a document since a document is intended to be understood as a whole and data items about an individual are usually scattered across different documents.
is an aggregate of ICEs also an ICE? yes Is part_of the appropriate relation to use for data items and documented identities?
documented identity
I order a beer and the bartender authenticates my age by looking at my DOB on my driver's license. I sign into my email account, and the system authenticates my permission to read the email by checking the password I enter against my password listed in the database.
Authentication is the act of checking or verifying an identity claim (that is either tacit or explicit).
authentication
A role that inheres in a concretization of an identity document and is realized by an authentication process.
credential role
my filling in an immigration form, a judge's signing and stamping a court order
A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document.
deontic document act
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
a judge's role of signing a court order
A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a document act.
document act performer role
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
A document that explains all relevant study information to assist a human subject in understanding the expectations and requirements of participation in a research study. This form document is presented to and signed by the study subject.
The term definition is adapted from NCIt definition of 'consent form' (C16468) with modification. Compared to the NCIt definition, the ICO definition does not restrict the form to a clinical trial.
a planned process that involves the design of an informed consent form.
an organization that approves the clinical study protocol, and ensures the applicable governing rules and laws are upheld.
a planned process that is a study requiring an official informed consent process.
study requiring informed consent
a role that inheres in a patient or the legal guadian when he/she participates the consenting process.
consenter role
A character string that is assigned by the review board upon approval of the study.
For the review board approval, different countries or continents may have different responsible entities for approving the study. For example, in USA, the board is called "Institutional Review Board" (IRB). In many countries in Europe, it is called Ethics committee.
This term definition is adapted from the definition of the NCIt term 'Review Board Approval Number Text'.
YL, EE, YH, AK, MH
review board approval number
an informed consent form that is used for vaccination
vaccination informed consent form
a textual entity that provides a question in text.
question textual entity
A questionaire that is filled up with answers.
filled questionnaire
a textual entity that answers a question with an option.
answer option text entity
an answer option textual entity that answers a question with a yes.
yes answer text entity
an answer option textual entity that answers a question with a no.
no answer text entity
a planned process that involves the filling of an informed consent form.
filling informed consent form
a planned process that involves the filling of a questionnaire form that includes a list of questions.
filling questionnaire
A dependent continuant which is about a portion of reality.
A representation which specifically depends on an anatomical structure in the cognitive system of an organism.
negative-sense genome single-stranded RNA viruses
Cell-associated subacute sclerosing panencephalitis
Subacute sclerosing panencephalitis virus
subacute sclerosing panencephalitis virus, SSPEV
purple photosynthetic bacteria and relatives
Mycobacterium tuberculosis typus humanus
ssRNA positive-strand viruses, no DNA stage
Diplokokkus intracellularis meningitidis
Micrococcus meningitidis cerebrospinalis
Enterobacteraceae (ex Lapage 1979) Lapage 1982, fam. nov., nom. rev.
Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980, fam. nov., nom. rev.
Yersinia pseudotuberculosis subsp. pestis
Salmonella enterica subsp. enterica serovar Typhi
Bacillus/Lactobacillus/Streptococcus group
a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event.
Melanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'.
YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device.
YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention.
YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events.
YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'.
WEB: http://en.wikipedia.org/wiki/Adverse_event
WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm
WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068
The OAE official website is: http://www.oae-ontology.org/.
medical intervention is a planned process that has the goal of diagnosing, preventing or relieving illness or injury.
The act of intervening, interfering or interceding with the intent of modifying the outcome. In medicine, an intervention is usually undertaken to help treat or cure a condition. For example, "Acupuncture as a therapeutic intervention is widely practiced in the United States," Reference: http://www.medterms.com/script/main/art.asp?articlekey=34214 . Some interventions can be used for diagnosis.
WEB: http://wiki.answers.com/Q/What_is_medical_intervention
an adverse event that occurs after a vaccination.
Surgery is a medical procedure that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury, to help improve bodily function or appearance. The key difference between a surgery and a general procedure is the need for an incision. Making an incision, or cutting into the skin to gain access to the body’s deeper tissues or organs, is a defining characteristic of surgery.
WEB: http://en.wikipedia.org/wiki/Surgery
WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm
a sensory capability AE that has an outcome of dizziness
Dizziness describes a number of subjective symptoms, which the patient may describe as feelings of lightheadedness, floating, wooziness, giddiness, confusion, disorientation or loss of balance. Medical terms include vertigo, disequilibrium, pre-syncope or syncoptic episode. Causes may stem from a variety of failures of equilibrioception, hypotension, cerebral hypoxia or a reaction to environmental chemicals or drugs.
a sensory capability AE that has an outcome of loss of consciousness, fainting
Syncope is the medical term for fainting, a sudden, usually temporary, loss of consciousness.
WEB: http://en.wikipedia.org/wiki/Syncope_%28medicine%29
WEB: http://en.wikipedia.org/wiki/Unconsciousness
a nervous system AE that has the symptom of GBS. Guillain-Barre syndrome (GBS) is a disorder in which the body's immune system attacks part of the peripheral nervous system. The first symptoms of this disorder include varying degrees of weakness or tingling sensations in the legs. In many instances, the weakness and abnormal sensations spread to the arms and upper body. These symptoms can increase in intensity until the muscles cannot be used at all and the patient is almost totally paralyzed. In these cases, the disorder is life-threatening and is considered a medical emergency. Usually Guillain-Barre occurs a few days or weeks after the patient has had symptoms of a respiratory or gastrointestinal viral infection. Occasionally, surgery or vaccinations will trigger the syndrome. Reference: http://www.ninds.nih.gov/disorders/gbs/gbs.htm.
WEB: http://www.ncbi.nlm.nih.gov/pubmed/23299621
serious adverse event is an adverse event that requires in-patient hospitalization, or prolongation of existing hospitalization, or that causes congenital malformation, or that results in persistent or significant disability or incapacity, or that is life threatening or results in death.
WEB: http://en.wikipedia.org/wiki/Serious_adverse_event
WEB: http://www.google.ca/url?sa=t&source=web&ct=res&cd=1&ved=0CA4QFjAA&url=http%3A%2F%2Fwww.irrd.ca%2Fethics%2Fimages%2FAdverse-event-definition.doc&ei=eqFMS-yFNZSoswOt6siKAQ&usg=AFQjCNGnQcwI8OXH7dqxwo4RgZEEn8X6lg&sig2=UNngkCdO5ZTFvbIB1pKuaA
a medical intervention that refers to any series of pre-defined steps that should be followed to achieve a desired result.
medical procedure
A data item that contains the outcome of a survey.
Alice Nzinga
survey data
A plan specification that is realized by process of gathering information (e.g. by asking questions).
survey plan specification
A planned process that realizes the concretization of a survey to generate an output(survey data.)
survey execution
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
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
Could add specific objective specification
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
GROUP: Role Branch
OBI
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
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.
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.
protocol
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
drug added to a buffer contained in a tube; substance injected into an animal;
material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
9 March 09 from discussion with PA branch
material to be added role
drawing a conclusion based on data
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
planning
The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
a process of creating or modifying a plan specification
7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
target of material addition role is a role realized by an entity into which a material is added in a material addition process
From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
target of material addition role
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
a planned process that carries out a study design
a planned process that realizes the concretization of a study design
removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate.
09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity.
A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
Need to clarify if this is a document or a directive information entity (or what their connection is))
PERSON: Jessica Turner
Merriam-Webster
An information content entity that is inferred from data.
In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
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 planned process that produces output data from input data.
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
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.
dialysis
the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
PERSON:Kevin Clancy
The genome of an organism of Proteobacteria
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 disorder that involves some structural damage that is immediately caused by a catastrophic external force.
At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level.
http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5 OGMS call adoption- 16 SEPT 2015 https://docs.google.com/document/d/1iiV1-fTS7BUUSzDw3N_Afx42698YWf54-FOTY2NkAxo/edit
creation date: 2011-09-20T09:57:44Z edited date: 30 SEPT 2015
Social Security Number(SSN) is a Centrally Registered IDentifier that is a nine-digit number issued to U.S. citizens, permanent residents, and temporary (working) residents under section 205(c) of the Social Security Act, codified as 42 U.S.C. § 405(c). The number is issued to an individual by the Social Security Administration, an independent agency of the United States government. Its primary purpose is to track individuals for Social Security purposes.
social security number
A social role inhering in a human being.
human social role
party to a legal entity
party to a legal proceeding
party to a legal agreement
party to a marriage contract
party to a power of attorney
A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture.
gender role
A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question.
male gender
male gender role
A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question.
female gender
female gender role
A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis.
health care role
A health care 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 health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism.
health care provider role
A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments.
physician
physician role
A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life.
nurse
based on: http://en.wikipedia.org/wiki/Nursing
nurse 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
obsolete person health care provider role
A health care provider organization role that inheres in an organization consisting of two or more physicians.
physician practice
A role borne by an organization and realized by providing healthcare services by healthcare professionals of multiple different disciplines of medicine and enabling stationary treatment.
hospital
obsolete_hospital role
A health care provider organization role that inheres in an organization that is comprised of other organizations.
integrated delivery network
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 inhering in an entity realized by social interactions in human society.
Previous definition: A role played by an entity in human social processes.
obsolete role in human social processes
A role in human social processes that inheres in an organization.
Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants.
organization social role
A role in human social processes that inheres in an organism.
William R. Hogan Mathias Brochhausen
Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc.
Previous definition: A role in human social processes played by an organism.
organism social role
An organization social role that, 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
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).
geopolitical organization
geopoli organization
A patient role that inheres in a human being.
human patient role
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.
major administrative subdivision
obsolete 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.
geopolitical dependency
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).
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
An aggregate of sovereign states that share some feature in common, but is not an organization nor necessarily the outcome of some treaty among them.
An aggregate of geopoli organizations that is not itself a sovereign state and whose members are only sovereign states that have some feature in common
aggregate of sovereign states
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 geopoli organizations
obsolete aggregate of geopoli organizations
An aggregate of geopoli organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common.
aggregate of dependencies
An aggregate of geopoli organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common
aggregate of major administrative subdivisions
obsolete aggregate of major administrative subdivisions
A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law.
Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
We are aware of the fact that Wikipedia's definition differs from ours by saying that "Legal personality (...) is the characteristic of a non-living entity regarded by law to have the status of personhood" (http://en.wikipedia.org/wiki/Legal_personality) However, Shaw explicates: "In any legal system, certain entities, whether they be individuals or companies, will be regarded as possessing rights and duties enforceable at law. Thus an individual may prosecute or be prosecuted for assault and a company can sue for breach of contract. They are able to do this because the law recognises them as 'legal persons' possessing the capacity to have and to maintain certain rights, and being subject to perform specific duties. (...) In municipal law individuals, limited companies and public corporations are recognized as each possessing a distinct legal personality, the terms of which are circumscribed by the relevant legislation" (Shaw MN: International Law. Sixth Edition. Cambridge University Press, Cambridge, 2008). We hold that Shaw's position is ontological more prolific since it not only allows to explain how groups of individuals become recognized as unities at law, but also how different individuals can hold different legal personality roles (always against the context of one legal system). The latter will proof useful when dealing with the representing comatous patients or minorsat law in ontologies.
legal person role
A role that inheres in an organism and is realized by habitually smoking tobacco products.
smoker role
intravenous drug user
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
intergovernmental organization
"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
Katrina Donovan
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
a geopolitical organization that is voluntary and private, whose members are individual persons or organizations that come together to acheive a common purpose.
nongovernmental organizations
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.
private governance organizations
"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.
Examples: private bond-rating agencies such as Moody's Investors Service, International Chamber of Commerce, Worldwide Responsible Apparel Manufacturing Principles, Forest Stewardship
obsolete private governance organizations
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.
nation
nation state
sovereign state
Per Wikipedia, the word 'nation' does not always refer to soverign states. For example, the "nation of Islam".
a governmental organization that has a local, regional, or territorial government that recognizes a sovereign state as its higher political authority
subnational entity
supranational entity
material entity role
organism role
Homo sapiens role
organization role
A function inhering in a material entity that, if realized, is realized by the material entity being the site at which inpatient and outpatient healthcare is provided to a patient population.
hospital function
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 health care facility that bears the function to provide acute and intensive healthcare services and that is run by a hospital organization and is the bearer of a hospital function.
William Hogan
hospital facility
A facility that is run by a school organization and is the bearer of a school function.
school facility
secondary school role
A trauma patient role that inheres in a homo sapiens who is under the age of 15 years.
pediatric trauma patient
The following definition for 'pediatric trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. "A trauma patient who is under the age of 15 years."
pediatric trauma patient role
A patient role that inheres an organism suffering one or more injuries.
injured patient
The following definition for 'injured patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient suffering one or more injuries.
injured patient role
A patient role that inheres in an organism suffering a thermal, electrical, chemical or radiation burn.
The following definition for 'burn patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient suffering a thermal, electrical, chemical or radiation burn.
burn patient
burn patient role
A physician role that is created by training and certification in rehabilitation/physical medicine and that is realized by the provision of or supervising of the provision of rehabilitation or physical therapy to a patient.
physiatrist
The following definition for 'physiatrist' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A physician with training and certification in rehabilitation/physical medicine.
Definition updated May 5, 2016. Original definitions was, a health care role borne by a human being and realized by training and certification in rehabilitation medicine.
physiatrist role
A patient role that inheres in an organism with some non-superficial traumatic injury. The role is realized by admision to a hospital, transfer from one hospital to another for the purpose of trauma care, or has death as a result of the traumatic injury.
trauma patient
The following definition for 'trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient sustaining an injury who has been admitted to the hospital, transferred from one hospital to another for the purpose of trauma care, or has died as a result of the traumatic injury.
trauma patient role
A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function.
Housing units are individuated by their residence functions.
housing unit
A function that inheres in a material entity and, if realized, is realized by protecting persons and their possessions from weather and by some person or group of persons habitually sleeping in at least one site that is contained by that material entity.
residence function
A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of that housing unit's residence function.
Note in OMRSE it is the housing unit, not the people living there, that are the bearers of a "residence function". Note the distinction between being a residence and a resident.
Note that it is not possible in OWL 2, at least that we have yet found, to say that the housing unit in which the process occurs is the same one that is the bearer of the residence function (that the process realizes).
household
A role in human social processes that, if realized, is realized when the bearer provides labor or services in exchange for a wage or salary as specified by some deontic declaration.
job role
workplace facility
a function inhering in a material entity that, if realized, is realized by that material entity being the site where the work of some organization is carried out
workplace function
A US Census householder role is a human social role that, if realized, is realized by that person being a member of a household and either owning or renting the housing unit in which that household resides and being designated as the householder. If there is only one member of the household who owns or rents the housing unit, that person is designated the householder by default.
http://www.census.gov/cps/about/cpsdef.html last accessed on June 30, 2015
US census householder role
A US cenus reference person role is a human social role that inheres in a Homo sapiens who is a member of a household and is realized by other persons in the household being recorded in the US census in relation to that person.
http://www.census.gov/cps/about/cpsdef.html last accessed June 30, 2015
US Census reference person role
An ethnic identity datum that is the output of an ethnic identification process that uses OMB terminology for ethnicity or terminology that is mapped the OMB ethnicity terms.
OMB ethnic identity information content entity
obsolete OMB ethnic identity datum
enrollment end date
A role that concretizes a socio-lega generically dependent continuant
obsolete socio-legal human social role
A human social role that is created by a deontic declaration performed by an organization.
human organizational role
human role within an organization
a role in human social processes that is realized when the bearer provides a wage or salary in exchange for some labour or services as specified by some declaration
employer role
age measurement datum
A document that records a legally binding agreement between two or more parties.
A contract is a document that is the specified output of a legally binding document act and records a legally binding agreement between two or more parties.
contract
A contract by which one party secures the other against pecuniary loss by payment of a sum of money if a specified event occurs.
indemnity contract
An indemnity contract that distributes risk among a group of people
insurance policy
A role that inheres in an organism that is able to receive benefits from an insurance policy. The role, if realized, is realized by receiving benefits that are covered by the insurance policy.
insured party role
An organization that secures a group of people against pecuniary loss by payment of a sum of money if a a specified event occurs.
insurance organization
An insured party role that inheres in a person who participates in the creation of the insurance contract and is eligible to receive benefits as specified by the insurance contract.
policy holder role
payer role
party to an insurance policy
enrollment start date
A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
racial identity information content entity
obsolete racial identity datum
racial identification process
An ethnic identity datum is an information content entity that is the output of some ethnic identitification process and is intended to be a truthful statement about the cultural or national heritage of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
ethnic identity information content entity
obsolete ethnic identity datum
ethnic identification process
A facility bearing the function to provide healthcare and that is administered by a health care organization for the purpose of providing health care to a patient or patient population.
health care facility
A human social role that inheres in a human who is legally eligible to work, is conferred by the U.S. Census Bureau, and is realized by the bearer not working and either making active efforts to find employment in the four weeks prior to the reference week or waiting to be recalled from temporary layoff.
US Census unemployed role
A health care facility that bears a function to provide healthcare to the sick or terminally ill
Emma Norris
Human Behaviour Change Project
hospice facility
skilled nursing facility
A facility to assist in physical or addiction recovery
rehabilitation facility
A facility that is run by a nursing home organization and is the bearer of a nursing home function.
nursing home facility
A community living health care facility that provides health care services in a home-like setting
residential health care facility
overnight dialysis facility
A health care facility that bears a function to provide low intensity healthcare services to patients on a short-term basis, with patients leaving on the same date as arriving (i.e., without them staying overnight)
Broadened from treatment to healthcare services generally. "Low intensity" is not defined at the moment, but is needed to differentiate from same-day surgery centers or observation stays in hospitals that last <24 hours. The idea is that few invasive procedures are performed, and the ones that are invasive are not typically much worse than a blood draw. Maybe bone marrow biopsy is as aggressive as it gets. I wonder if hematologists do that on an outpatient basis.
outpatient clinic facility
physician office facility
ambulatory surgery facility
urgent care facility
A health care facility that bears a function to provide emergency healthcare services and the acute care of patients who present without prior appointment, having arrived either by their own means or by ambulance
Adapted from Human Behaviour Change Project
emergency department facility
urgent care function
ambulatory surgery function
hospice function
emergency department function
physician office function
outpatient clinic function
overnight dialysis function
rehabilitation function
skilled nursing function
residence function (OMRSE:00000075)
obsolete residential function
nursing home function
A deontic document act that concludes an inpatient encounter.
discharge process
patient discharge
An OMB ethnic identity datum that indicates the person identified is of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race.
OMB Hispanic or Latino identity information content entity
obsolete hispanic or latino identity datum
An OMB ethnic identity datum that indicates the person identified is not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race.
OMB not Hispanic or Latino identity information content entity
obsolete not hispanic or latino identity datum
A human health care provider role that inheres in a human being that is created by state licensing and that is realized by taking patient histories, performing physical exams, diagnosing illnesses, developing treatment plans, ordering lab tests, prescribing medications, counselling and educating patients, suturing wounds, and assisting in surgery under the supervision of a physician or a surgeon.
US physician assistant role
A physician role that inheres a human being and, if it is realized, is realized either by administering medication for the temporary general or local suppression of sensory or motor nerve function during some health care encounter or by making decisions independently of a supervising physician regarding the adminstration of such medication.
anesthesiologist role
obsolete OMB racial identification process
An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method.
social identity information content entity
obsolete identity datum
A gender identity is an information content entity that is the output of some gender identitification process and is intended to be a truthful statement about a person's subjective sense of their gender. Unlike data items they are not necessilary contributed or acquired by a reliable method.
gender identity information content entity
obsolete gender identity datum
identification process
gender identification process
a gender identity datum resulting from a gender identification process in which ‘female’ is selected based on the participant's subjective sense of gender
female gender identity information content entity
obsolete female gender identity datum
A physician role that, if realized, is realized by its bearer using operative manual and instrumental techniques to investigate, treat, or modify a patient's anatomical or physiological state for health, functional, or aesthetic purposes.
surgeon role
A surgeon role realized by its bearer using performing neurosurgery.
neurosurgeon role
a gender identity datum resulting from a gender identification process in which ‘male’ is selected based on the participant's subjective sense of gender
male gender identity information content entity
obsolete male gender identity datum
An information content entity that is about human travel.
human traveling information
A symbol that denotes a specific household
household identifier
family identifier
an identity datum that has been asserted by the person whom it is about
obsolete self-identity data item
A planned process in which the bearer of an employer role provides wages or salary to the bearer of an employee roll in fullfillment of the arrangements specified in some declaration
employment process
A surgeon role that, if realized, is realized by its bearer by performing procedures on a child.
pediatric surgeon role
a facility that is run by an adult foster home organization and is the bearer of an adult foster home organization
adult foster home facility
adult foster home function
a health care facility that also bears a residence function and thus one in which the patients are also residents of the facility
community living health care facility
registered nurse role
skilled nursing encounter
They include assistance with activities of daily living, assistance with instrumental activities of daily living, medication assistance, and health support http://ahca.myflorida.com/Medicaid/acs/index.shtml
assistive care encounter
assistance with activities of daily living care encounter
assistance with instrumental activities of daily living encounter
medication assistance care encounter
A facility that is run by an assisted living facility organization and is the bearer of an assisted living facility function.
assisted living facility
assisted living function
temporally located after some acute care encounter Somehow involves skilled nursing encounters
post-acute health care encounter
acute care encounter
A process (1) where the active participant, who at the beginning of the process is located in a healthcare facility, exits the facility and no longer stands in a "located in" relationship to the facility and (2) is immediately preceded by a healthcare encounter in which the active participant also participated.
leaving a health care facility after receiving care
obsolete medical advice
Note that not all responses to a question asking process are answers. For example, a refusal to answer is not an answer. A refusal to answer is also not a specified output of the question asking process since it does not acheive the objective of asking the question, which is to get an answer.
response to a question asking process
home health care organization
home health care function
home health care encounter
obsolete questions asking process
palliative function
palliative care encounter
hospice organization
health care function
obsolete material information bearer of question text plus answer set
refusal to answer datum
response to an identity question asking process
obsolete identity question asking process
obsolete ethnic identity question asking process
obsolete race identity question asking process
answer to identity question
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment.
OMB American Indian or Alaska Native identity information content entity
obsolete American Indian or Alaska Native identity datum
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent.
OMB Asian identity information content entity
obsolete Asian identity datum
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the black racial groups of Africa.
OMB black or African American identity information content entity
obsolete black or African American identity datum
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands.
OMB Native Hawaiian or other Pacific Islander identity information content entity
obsolete Native Hawaiian or other Pacific Islander identity datum
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Europe, the Middle East, or North Africa.
OMB white identity information content entity
obsolete white identity datum
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms.
OMB racial identity information content entity
obsolete OMB racial identity datum
A role that inheres in an organism and is realized by habitually smoking 10 or more tobacco cigerettes a day or the equivalent in other tobacco products.
heavy smoker role
A role that inheres in an organism and is realized by habitually smoking 1>10 tobacco cigerettes a day or the equivalent in other tobacco products.
light smoker role
answer set
question text
option as member of some answer set
residential facility
A facility that has at least one housing unit as part in which a person or persons live
Modified version of definition provided by Human Behaviour Change Project
A process in which some participant shares some information content entity about some state of that participant with some other participant.
The term 'participant' in the definition need not refer to a human agent.
obsolete communication
A disposition inhering in a material entity that, if realized, is realized by that material entity’s communicating via some linguistic concretization.
obsolete linguistic competence
A disposition inhering in a linguistic community that (i) is a maximal aggregate of communicatively compatible linguistic competences, and (ii) if realized, is realized by any and all realizations of those linguistic competences.
obsolete language
A maximal aggregate of material entities such that each member bears a linguistic competence for the same language.
linguistic community
A communication in which some participant states a preference for some communicative process to be in a certain language, and that has a concretization of a preferred language information content entity as its specified output.
obsolete expression of preferred language
An information content entity that (i) is about some person, some language, and some linguistic competence; and (ii) conveys the language with which that person prefers to communicate within some given context.
obsolete preferred language information content entity
a communication in which some participant requests of some other participant an information content entity about some portion of reality
As with the parent class, 'participant' in the definition need not refer to a human agent.
The medium and grammatical form are irrelevant. For example, the request may be written or spoken, and while it may be in the form of a question, it need not be.
information content entity-request process
an information content entity-request process in which some participant requests of some other participant an information content entity that indicates the ethnic identity of that other participant
information content entity request about ethnic identity
an information content entity-request process in which some participant requests of some other participant an information content entity that indicates the racial identity of that other participant
information content entity request about racial identity
A deontic document act in which a patient is registered with a health care provider for the purpose of receiving care in an inpatient encounter.
admission process
cancer summary staging
The cancer summary staging performed on patient John Doe's clinical picture.
A planned process of determining the extent to which a cancer disease has developed by growing and spreading throughout an organism.
tumor summary staging
cancer summary staging code
The cancer summary staging code that is the outcome of the cancer summary staging performed on patient John Doe's clinical picture.
An information content entity that is the specified output of cancer summary staging.
tumor summary staging code
An information content entity that is intended to be a truthful statement about some person and whether that person identifies as some particular aspect of social identity—such as a gender, an ethnicity, a race, or a sexual orientation—where the sense of identifying may correspond to either (i) an aspect of one’s cognitive representation of oneself, (ii) how one prefers to be regarded by others within some social context, or (iii) how one chooses to present oneself to others within some social context.
Sarah Bost
We include (i)-(iii) to acknowledge that there are different senses of "identify" that are relevant here, and that we may not always be sure which sense the person concretizing the social identity information content entity intended. While (i) concerns how one thinks of oneself, (ii) and (iii) are more focused on one's interactions with others. Importantly, some choose not to share with others how they identify in the sense of (i). For example, one can consider oneself to be some certain gender without either wanting others to know or choosing to present oneself in a corresponding way. We distinguish (ii) and (iii) because one can prefer to be regarded some certain way without attempting to present oneself in any corresponding way.
A social identity information content entity that is about whether some person identifies as some ethnicity.
Ethnicity is separate from but related to racial identity. It refers more to identifying with a particular culture than with individuals similar in physical appearance. It includes things like Hispanic ethnicity (which spans many nations) and national cultural identities like Irish and ethnic groups within nations such as Catalan and Armenian.
An ethnic identity information content entity that uses OMB terminology for ethnicity or terminology that is strictly mapped onto the OMB ethnicity terms.
OMB dichotomizes ethnicity into Hispanic or Latino and Not Hispanic or Latino, and ignores all other forms of ethnicity.
obsolete OMB ethnic identity information content entity
An OMB ethnic identity information content entity that is about some person's identifying as Hispanic or Latino, which are intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race.
It comprehends people of Portuguese culture or origin in Brazil.
obsolete OMB Hispanic or Latino identity information content entity
An OMB ethnic identity information content entity that is about some person's identifying as neither Hispanic nor Latino, which are intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race.
obsolete OMB not Hispanic or Latino identity information content entity
A social identity information content entity that is about whether some person identifies as some gender.
A gender identity information content entity that is about some person's identifying as female in gender.
A gender identity information content entity that is about some person's identifying as male in gender.
A gender identity information content entity that is about some person's identifying as non-binary in gender.
non-binary identity information content entity
A social identity information content entity that is about whether some person identifies as some race.
A racial identity information content entity that uses OMB terminology and definitions for race or terminology that is strictly mapped onto the OMB race terms.
obsolete OMB racial identity information content entity
An OMB racial identity information content entity that is about some person's identifying as American Indian or Alaska Native, which is intended to mean having origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment.
This definition corresponds to that used by OMB. It is worth noting that the OMB definition from which this one is derived is problematic, in that it implies that one's race cannot be Native American or Alaskan Native unless one maintains tribal affiliations or community attachment.
obsolete OMB American Indian or Alaska Native identity information content entity
An OMB racial identity information content entity that is about some person's identifying as Asian, which is intended to mean having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent.
obsolete OMB Asian identity information content entity
An OMB racial identity information content entity that is about some person's identifying as black or African American which is intended to mean having origins in any of the black racial groups of Africa.
obsolete OMB black or African American identity information content entity
An OMB racial identity information content entity that is about some person's identifying as Native Hawaiian or other Pacific Islander, which is intended to mean having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands.
obsolete OMB Native Hawaiian or other Pacific Islander identity information content entity
An OMB racial identity information content entity that is about some person's identifying as white which is intended to mean having origins in any of the original peoples of Europe, the Middle East, or North Africa.
obsolete OMB white identity information content entity
A social identity information content entity that is about whether some person identifies as having some sexual orientation.
sexual orientation identity information content entity
An information content entity that is about some geographical region, in which a postal delivery route denoted by a particular ZIP code is realized, and that is the specified output of a disclosure of residence.
Hansi Zhang
residence ZIP code information content entity
debt obligation
Three Arrows Capital declared bankruptcy on July 1, 2022 after defaulting on a $665 million debt obligation owed to Voyager Digital.
A directive information entity that prescribes that something will be transferred from some human or organization that is the bearer of a duty holder role to another human or organization that is the bearer of a claimant role.
A social act that creates an information content entity that is about some geographical region in which a human being dwells.
disclosure of residence
A data set whose members are obtained from one or more electronic health records.
EHR data set
Mathias Brocchausen
electronic health record data set
A data set whose members are the specified output of some process of adjudicating health care insurance claims (and whose inputs are at least partly some members of a health care billing data set).
It covers prescription claims because pharmacies bill insurance companies for patients’ prescriptions via submitting insurance claims.
The insurance claim is submitted to the insurance company by either the patient or the provider. It is not necessarily always the provider, although in the United States, it typically is.
The outcome of the adjudication of a claim in the claims dataset could be favorable or unfavorable for the healthcare provider, the patient, or both. The idea is just that they’ve been adjudicated, one way or the other (or anything in between if that’s a possibility).
The reason we say billing data are only part of the input is because we are not conflating the insurance claim with the bill. It is our understanding that the provider’s bill of services is either part of the claim or “attached” to it in some manner, but doesn’t constitute the entire claim itself.
The sources of these data are held by insurers or other health plan providers.
health care claim data set
A data set whose members are obtained from billing-related data sources that (i) are generated by a health care organization as a result of internal administrative processes, and (ii) are about services rendered or materials used during some health care encounter.
health care billing data set
Recording data in an EHR. Financial tasks for a healthcare organization. Scheduling shifts for health care workers.
A planned process (i) that is neither a health care process nor an ancillary health care process, and (ii) in which some employee of a health care organization manages, or helps to manage, the performance of tasks that realize the functions of that organization.
health care administrative process
A health care administrative process that has as input a diagnosis, and has as output a value indicating that diagnosis is about the condition that prompts the admission process that starts the encounter during which the diagnostic process that outputs that diagnosis begins.
principal diagnosis-assignment process
A health care administrative process that has as input a diagnosis, and has as output a value indicating that diagnosis is about an underlying condition that is distinct from the condition that prompts the admission process that starts the encounter during which the diagnostic process that outputs that diagnosis begins.
secondary diagnosis-assignment process
The Alachua county smoking survey plan specification.
A survey plan specification that aims to collect information about the smoking behavior or lack thereof of a population on a county level. Concretization of a smoking survey plan that is stratified by county.
Jiang Bian
county smoking survey plan specification
The Alachua county smoking survey execution.
A survey execution that realizes the concretization of a smoking survey plan specification that is stratified by county.
county smoking survey execution
The Alachua county smoking survey data.
Survey data that is the specified output of a county smoking survey execution.
county smoking survey data
Calculating the Alachua County smoking rate from Alachua County smoking data.
A data transformation that has data about the smoking status of a population as its specified input and a percentage or ratio of smokers in that population as a specified output.
smoking rate calculation
The Alachua County smoking rate.
A data item that is the specified output of a smoking rate calculation that has data about smoking behavior or lack there of on a county level.
county smoking rate data
money
Todd does not have enough money to buy more plants at the horticultural club's poinsettia sale.
A debt obligation between two parties that has part a scalar value specification and whose concretizations indicate that their bearers can be used in a financial transaction or payment of debt, or as a measure of the value of some entity in a financial valuation process or prospective financial valuation process.
currency
US currency is an accepted form of legal tender, not just in the United States, but in many countries around the world, such as El Salvador.
A material entity that is the bearer of a concretization of money and is created by some governmental organization or on behalf of some governmental organization that has authorized its creation.
exchange of ownership
Tom exchanged ownership of his computer for Tina's scooter.
A planned process whereby one agent (or active participant) or a group of agents transfer ownership of some property to another agent (or active participant) or group of agents in the process, who in return transfer ownership of some their property to the first agent (or active participant).
barter
financial transaction
Apple acquired semiconductors from Samsung in a financial transaction yesterday.
A planned process whereby one participant partly or completely fulfills an obligation to another participant by transferring ownership of some other debt obligation, which is typically money.
monetary transaction
payment of debt
I made a debt payment with my credit card company yesterday and no longer owe them money.
A planned process whereby ownership of some entity of value is transferred by one participant to another to fulfill some obligation, on their behalf, after some service is performed or the ownership of some entity is exchanged.
financial valuation process
The financial valuation of Ravi's car today determined that the car is worth $2000.
A planned process that has as specified output some scalar measurement datum that is about an entity—such as a material good or a service—and is measured in terms of the quantity of some other material entity.
prospective financial valuation process
The prospective valuation of my company's stock indicates strong optimism for our financial growth over the next few years.
A planned process that has as specified output some predicted value that is about an entity—such as a material good or a service—and is measured in terms of the quantity of some material entity at some point in the future.
Relational quality inhering in persons by virtue of being each other’s spouse, boyfriend/girlfriend, dating partner, or ongoing sexual partner.
intimate partnership
Behavior that is cruel, violent, demeaning, or invasive.
abusive behavior
Abusive behavior in which the aggressor does or attempts to do the following: mentally or emotionally harm or exert control over another.
psychologically abusive behavior
Abusive behavior in which the aggressor does or attempts to do the following: harm, restrain, or coerce another through physical force.
physically abusive behavior
Abusive behavior in which the aggressor does or attempts to do the following: force or coerce another to participate in a sexual act to which the latter has not freely given consent.
sexually abusive behavior
A health care provider role that is realized in maintaining the health of a human being during their pregnancy and both them and the neonate during labor, delivery, and postpartum.
skilled birth attendant role
birth attendant role
An information content entity that conveys that a particular person has a linguistic competence for a particular language
Barry Smith
Jobst Landgrebe
linguistic competence information content entity
A linguistic competence information content entity that conveys the language is the one for which the person has their most proficient linguistic competence.
primary language information content entity
A linguistic competence information content entity that conveys the person uses the language at home.
language-at-home information content entity
A social act or aggregate of social acts that include some worship, prayer, or proselytizing.
religious gathering
A count of the number of patients that some hospital facility has the capacity for.
hospital bed capacity data item
A data item that is the output of some data transformation that takes as input the number of individuals in a population who are occupation holders and has as output the proportion of those individuals who are classified by the European Skills, Competences, Qualifications and Occupations as door-to-door sales worker, news or street vendors; building cleaning workers; pressers, textile, garment, or related materials; septic tank servicers or sewer pipe cleaners; farmworkers or laborers, crop, nursery, or greenhouse; farmworkers, farm, ranch, or aquacultural animal; agricultural workers, all other; landscaping or groundskeeping workers; grounds maintenance workers, all other; forest or conservation workers; logging workers, all other; fishing or hunting workers; helpers--extraction workers; extraction workers, all other; helpers, construction trades; rail-track laying or maintenance equipment operators; construction laborers; helpers--production workers; production workers, all other; laborers or material movers; refuse or recyclable material collectors; couriers or messengers; material moving workers, all other; aircraft cargo handling supervisors; first-line supervisors of helpers, laborer, or material mover, hand; first-line supervisors of transportation worker, all other; tank car, truck, or ship loaders; cooks, fast food; cooks, short order; food preparation workers; dining room or cafeteria attendants or bartender helpers; dishwashers; food preparation or serving related workers, all other; personal care or service workers, all other; baggage porters or bellhops; maintenance or repair workers, general; installation, maintenance, or repair workers, all other; meter readers, utilities; coin, vending, or amusement machine servicers or repairers; motion picture projectionists; ushers, lobby attendants, or ticket takers; amusement or recreation attendants; locker room, coatroom, or dressing room attendants; and parking attendants.
Currently, the Occupation Ontology (OccO ) only represents occupations as they are defined by O*NET. We define this class extentionally according to the O*NET-defined occupations that map to occupations in ESCO that are classified as elementary occupations.
proportion of population in an elementary occupation
A policy holder role that inheres in a person who participates in the creation of an insurance policy with a US state Medicaid agency.
Medicaid policy holder role
An insurance organization that is privately owned and that participates in the creation of insurance policies in return for some money from the policy holder.
insurance company
A policy holder role that inheres in a person who participates in the creation of an insurance policy with an insurance company.
private insurance policy holder role
A government organization that administers a given US state's Medicaid program by participating in the creation of insurance policies with eligible people and by participating in some payment of debt for a specified aggregate of health care encounters, specified processes (e.g, treatments, diagnostic tests) that are part of those encounters, and material entities used or prescribed during the encounters (e.g., medicine, prosthetics, glasses).
US state Medicaid agency
A highest level of education data item that represents the fact that an individual in the United States is has not achieved a level of education that is equivalent to or higher than a complete high school education.
highest level of education is below high school completion or equivalent data item
An information content entity that characterizes some aggregate of entities as partitioned into distinct subgroups, thereby demarcating them as categories.
categorization scheme
A categorization scheme that divides humans into groups considered by themselves or others as distinct on the basis of assumed common characteristics.
social categorization scheme
A highest level of education data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some undergraduate coursework, but without attaining an undergraduate degree.
highest level of education is some college data item
A collection of humans demarcated by some social categorization scheme.
social category
A social categorization scheme based on characteristics assumed to be biologically hereditary and to result in part from common locality of ancestors.
racial categorization scheme
A social category demarcated by some racial categorization scheme.
racial group
racial category
A social categorization scheme based on characteristics that are primarily cultural—such as ancestry, history, national or tribal background, cultural attachments or traditions, past linguistic heritage, religious affiliations, caste, or claimed kinship.
ethnic categorization scheme
A social category demarcated by some ethnic categorization scheme.
ethnic group
ethnic category
Communication in which a person reports some data items about either that person or another person.
personal data disclosure
A cognitive representation in which the representation’s bearer is represented as being its bearer.
subjective representation
A subjective representation of its bearer as being a member of some social category.
social identity
A social identity for which the category is a racial category.
racial identity
A highest level of education data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some high school coursework, but without attaining a diploma or equivalent.
highest level of education is some but not all high school data item
A social identity for which the category is an ethnic category.
ethnic identity
A social identity for which the category is also a behaviorally distinct group defined by its members degree of participation in some type of behavior.
behavioral identity
A highest level of education data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of high school or equivalent.
highest level of education is completion of high school or equivalent data item
A disposition that, if realized, is realized when the bearer intends to, and does, exercise abilities and skills in pursuit of obtaining or maintaining an job role.
Damion Dooley
Jie Zheng
John Beverley
John W. Judkins
Sam Smith
William D. Duncan
Yongqun He
occupation disposition
A process in which an occupation holder participates that realizes either an occupation disposition or job role.
occupation process
Eric Merrell
occupation activity
A human role within an organization that inheres in a person who has served in a branch of the U.S. military, is not currently serving in the U.S. military, and the person's service ended in accordance to conditions defined by the U.S. government.
38 U.S.C. §101(2), as well as “Determining Veteran Status” by the U.S. Department of Veterans Affairs (VA) Office of Small and Disadvantaged Business Utilization (OSDBU): https://www.va.gov/OSDBU/docs/Determining-Veteran-Status.pdf.
U.S. veteran role
A residence function that is realized only in processes in which eligible and approved residents participate, and that is a characteristic of a housing unit that is owned by a government and intended for use by seniors, people with disabilities, or those with low incomes.
public housing function
A role that inheres in a person who qualifies for public housing according to the criteria set forth by the relevant governmental entity and that is realized in processes that both have the person as a participant and realize the public housing function of some housing unit.
public housing eligibility role
A role that if realized, is realized by the bearer participating in human travel.
human traveller role
Matt Diller
See discussion at: https://github.com/mcwdsi/OMRSE/issues/191
human traveler role
A social categorization scheme based on the social identities assumed to be coincident of certain biological traits linked to reproduction and/or reproductive behavior.
gender categorization scheme
A social category demarcated by some gender categorization scheme.
gender group
gender category
A data item according to which a given person is a member of a given social category.
social category data item
A social category data item for which the social category is an ethnic category.
ethnic category data item
A social category data item for which the social category is a gender category.
gender category data item
A social category data item for which the social category is a racial category.
racial category data item
A social identity for which the category is a gender category.
gender identity
A social categorization scheme based on the social identities assumed as a result of a person's citizenship of a country.
A person may be a citizen of multiple countries at once, and a person's citizenship may change over time.
nationality categorization scheme
A social category data item for which the social category is a nationality category.
nationality category data item
A social category demarcated by some nationality categorization scheme.
nationality group
nationality category
A human role within an organization that itself bears a healthcare provider organization role.
human role within a healthcare organization
Colbie Reed
institutional health care provider role
Can be about any aspect of employment, such as salary, work location, or employer.
A data item that is about a person's job role and/or its realization.
employment data item
Chris Stoeckert
S. Clint. Dowland
job role data item
income data item
government assistance health care plan data item
health care plan data item
government assistance income data item
WIC data item
socio-economic data item
educating
A planned process with an active participant who acquires mental representations of information content entities (ICEs), which had no previous mental representation in the cognitive system, and through repeated use or application of these ICEs either (1) becomes the bearer of a new instance of some type of capability, and the participant was not previously the bearer of that instance of that type of capability, (2) "improves" an existing capability as demonstrated through realization(s) of that capability, and/or (3) loses a capability whose realization is considered negative.
learning process
An act of acquiring new information and repeatedly applying that information to develop a new skill, improve an existing skill, and/or losing a skill at doing something "bad".
An interesting question is whether there must be another participant who is the "educator". Some might object that many people are "self taught". A real case of being self taught is the first person who learned to play a stringed instrument, or to spin a ball on the tip of a finger. There was no previous information about that type of skill. The ICEs acquired are via one's sensory systems (vision, proprioception, auditory, etc.). On the other hand, in the case of those who are self-taught by reading books or watching videos, or acquiring some other form of ICEs concretized outside their brain, one argument might be that the author of those ICEs somehow "plays a role" in the education, although they cannot participate in the education process itself (If I read Aristotle, and through repeated application of the information I acquire through doing so, develop the ability to write better ontology definitions, surely Aristotle did not actively participate in my particular education process, although he did influence it in a very real way).
The loss of a "bad" capability is something like losing a bad golf swing and replacing it with a good one. Also a capability to disrupt the classroom might be something an educating process diminishes possibly to the point of "removal" in a student. This addition to the definition notwithstanding, we do not intend to incorporate the receipt of punishment into the definition of educating.
education process
educational objective specification
An objective specification that describes the type of capability or capabilities to be imparted or improved by its realization, which is an educating (education process).
An objective specification that describes the new knowledge & skill(s) to be obtained via an education process.
educational objective
educational plan specification
A plan specification with an educational objective specification as part.
A plan specification with one or more educational objectives.
Very broad. Covers everything from grade school to high school to college to graduate education, a MOOC, an individual course, a tutorial at a conference, a continuing education course or program, an informed consent video, etc, etc.
educational program
completing a program of education
An educating that realizes a concretization of some program of education.
Note that parent class 'educating' and referenced class 'program of education' are defined elsewhere in this education module of OMRSE.
This class refers extremely broadly to the successful realization of any program of education: a single course, first grade, MD, PhD, high school, the ninth grade, getting a black belt in karate, getting a master mechanic certification, a bachelor's degree, a masters degree, a graduate certificate, early childhood education program, and even getting a certificate at the end of some week-long workshop, summer camp, a certifcate from a cooking class, an actuarial certification.
early childhood education program
An educational program whose intended active participant, when a concretization of it is realized, is a human child of age birth to 8 years or a human fetus prior to birth.
pre-K education program
prekindergarten education program
preschool education program
early childhood education plan specification
primary education plan specification
An education plan specification with one or more primary education objective specifications as parts, and these are the only objective specifications it has as parts.
elementary education
In the united states, also called "elementary education"
It can still have action specifications as parts, and possibly other ICEs as parts. That's why we cannot say it has only primary education objectives as parts, and we have to introduce the double negative in the class axiom.
Primary education provides learning and educational activities typically designed to provide students with fundamental skills in reading, writing and mathematics (i.e. literacy and numeracy), and to establish a sound foundation for learning and solid understanding of core areas of knowledge and personal development, preparing for lower secondary education. It aims at learning at a basic level of complexity with little if any specialisation.
primary education program
primary education objective specification
An education objective specification that has a concretization that, when realized, results in the active participant's acquisition and development of fundamental skills in reading, writing and mathematics (i.e. literacy and numeracy).
By the end of primary education, the student has established a sound foundation for learning and solid understanding of core areas of knowledge and personal development, preparing for lower secondary education. It aims at learning at a basic level of complexity with little if any specialisation.
primary education objective
lower secondary education objective specification
An education objective specification that has a concretization that, when realized, confers to the active participant skills and knowledge in subject areas more specialized than basic reading, writing, and mathematics, with the overall goal of laying the foundation for lifelong learning and human development on which education systems may systematically expand further educational opportunities.
Examples of specific subjects could--but are not necessarily required to--include biology, history, science, literature, music, art. Programs at this level are usually organized around a more subject-oriented curriculum, introducing theoretical concepts across a broad range of subjects.
Programmes at ISCED level 2, or ‘lower secondary’ education, are typically designed to build upon the fundamental teaching and learning processes which begin at ISCED level 1. Usually, the educational aim is to lay the foundation for lifelong learning and human development on which education systems may systematically expand further educational opportunities. Programmes at this level are usually organized around a more subject-oriented curriculum, introducing theoretical concepts across a broad range of subjects.
lower secondary education objective
awarding of an academic degree
A deontic document act that has as specified output an academic degree and that confers on recipient of the academic degree the recognition and the claims and obligations that accompany the degree.
Different degrees have different claims and obligations associated with them. For example, having a medical degree (either M.D. or D.O.) entitles a person to sit for stage 3 of the US Medical Licensing Exam (otherwise one may not take the exam).
awarding an academic degree
basic education plan specification
An education plan specification that has as part both a primary educational objective specification and a lower secondary educational objective specification.
Most nations in the world mandate that children complete at least a basic education program. Some nations go further and include upper secondary education after basic education.
Whole range of educational activities, taking place in various settings, that aim to meet basic learning needs as defined in the World Declaration on Education for All (Jomtien, Thailand, 1990). According to ISCED standard, basic education comprises primary education (first stage of basic education) and lower secondary education (second stage). It also covers a wide variety of non-formal and informal public and private activities intended to meet the basic learning needs of people of all ages.
basic education program
lower secondary education plan specification
An education plan specification with one or more lower secondary education objective specifications as parts, and these are the only objective specifications it has as parts.
It can still have action specifications as parts, and possibly other ICEs as parts. That's why we cannot say it has only lower secondary education objectives as parts, and we have to introduce the double negative in the class axiom.
Requires successful completion of a primary education program as a pre-requisite.
lower secondary education program
upper secondary education objective specification
An educational objective specification that has a concretization that, when realized, confers on the active participant skills and knowledge that prepare them for tertiary education, or employment, or both.
Programmes at ISCED level 3, or ‘upper secondary’ education, are typically designed to complete secondary education in preparation for tertiary education, or to provide skills relevant to employment, or both. Programmes at this level offer students more varied, specialised and in-depth instruction than programmes at lower secondary education (ISCED level 2). They are more differentiated, with an increased range of options and streams available.
upper secondary education objective
upper secondary education plan specification
An education plan specification with one or more upper secondary education objective specifications as parts, and these are the only objective specifications it has as parts.
Requires successful completion of a lower secondary education program as a pre-requisite.
upper secondary education program
higher education plan specification
post-secondary education plan specification
post-secondary education program
Includes college, university, community college, professional schools (MD, RN, PharmD, PT, OT, DDS, dental hygienist, etc.), and so on.
Refers to all higher education beyond secondary education, and thus encompasses ISCED levels 5 and above, which will eventually be subclasses of this one.
Requires successful completion of a secondary education program as a pre-requisite.
higher education program
higher education objective specification
An educational objective specification that has a concretization that, when realized, confers on the active participant skills and knowledge in a specialized discipline, and culminates in the awarding of an academic degree.
post-secondary education objective
Refers to all education beyond secondary education that leads to the awarding of an academic degree.
higher education objective
vocational education objective specification
An educational objective specification that has a concretization that, when realized, is realized by a process that confers on the active participant knowledge and skills required to realize a particular type of employee role for a given occupation or trade.
Usually the skills are a major focus moreso than in other types of education. For example, auto mechanics, plumbers, and electricians.
vocational education objective
highest level of education socio-economic data item
A socio-economic data item that is about a person and their completion of at least some of the required courses of an education program, where the set of planned competencies to be acquired by completing that program, as a whole, are of a more advanced nature than the set of competencies acquired through any other educational program completed by the person.
Note that by 'more advanced nature' of the competencies, we do not mean merely having more knowledge, but rather a set of competencies / capabilities that enable the person to do things of a fundamentally different nature than before. This distinction is exemplified by the difference between a Masters and a PhD degree. The PhD has a key objective of enabling the person to function as an investigator in the domain, whereas a Masters does not.
This data item in a typical attribute-value system such as table, XML, JSON takes values like "secondary education", "Associate Degree", "Bachelor Degree", "High School", and so on. Also, note that we revised the definition in collaboration with our APRICOT project colleagues who noted that the individual need not have completed one of the education programs in a sequence, instead demonstrating competencies for admission to the highest level of eductation in some alternative way. For example, the highest level of education might be baccalaureate degree, but the individual did not graduate a secondary education program but instead got a General Educational Development (GED) certification / degree.
vocational education plan specification
An educational plan specification that has a vocational objective specification as part.
Vocational education programs are designed for learners to acquire the knowledge, skills and competencies specific to a particular occupation, trade, or class of occupations or trades. Such programs may have work-based components (e.g. apprenticeships, dual-system education programmes). Successful completion of such programs leads to labor market-relevant, vocational qualifications acknowledged as occupationally-oriented by the relevant national authorities and/or the labor market.
vocational education program
kindergarten education plan specification
A primary education plan specification that specifies the competencies and information content entities that should be acquired by students in the first year of primary education in the United States.
kindergarten education program
undergraduate higher education plan specification
A higher education plan specification that specifies the awarding of an associates or bachelors degree in the United States or equivalent degrees in other nations, and specifies as a pre-requisite the completion of some secondary education program.
undergraduate education program
undergraduate higher education program
graduate higher education plan specification
A higher education plan specification that specifies the awarding of a graduate certificate or degree, and specifies as a pre-requisite the awarding of an undergraduate degree.
graduate education program
Graduate degrees include masters, PhD, MD, PharmD, and other post-graduate professional degrees. To distinguish MS/PhD from the professional ones, subclass this class.
The prerequisite degree is at the bachelors level or equivalent. An associates degree is almost never sufficient for entry into graduate education programs.
graduate higher education program
highest level of education is completion of grades one through six socio-economic data item
A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is in the range of first through sixth grade.
Note: this broad, very loose level of grouping emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI. It indicates completion of some to all of primary education in the United States.
highest level of education is grades 1 through 6 data item
highest level of education is completion of grades seven through nine socio-economic data item
A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is in the range of seventh (7th) through ninth (9th) grade.
Note: this broad, very loose level of grouping emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI. It indicates completion of some to all of lower secondary education in the United States.
highest level of education is grades 7 through 9 data item
highest level of education is completion of grades ten through twelve socio-economic data item
A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is in the range of tenth (10th) through twelfth (12th) grade.
Note: this broad, very loose level of grouping emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI. It indicates completion of some to all of upper secondary education in the United States.
highest level of education is grades 10 through 12 data item
highest level of education is completion of some undergraduate degree socio-economic data item
A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some undergraduate degree.
Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.
highest level of education is completion of undergraduate degree data item
highest level of education is completion of some graduate degree socio-economic data item
A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some graduate certificate or degree.
highest level of education is completion of graduate certificate or degree data item
highest level of education is completion of some vocational education program socio-economic data item
A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some vocational education program.
highest level of education is completion of vocaational education program data item
highest level of education is completion of kindergarten socio-economic data item
A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is pre-kindergarten.
Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI. It indicates that a person has completed only early childhood education and nothing more.
highest level of education is completion of kindergarten data item
highest level of education is completion of pre-kindergarten socio-economic data item
A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is kindergarten.
highest level of education is completion of pre-kindergarten data item
language literacy competence
A disposition borne by a human being that (1) has a linguistic competence as a dispositional part and (2) if realized, is realized by the bearer's achievement of some personal goal.
human literacy
linguistic literacy
Xi Yang
Yonghui Wu
Other dispositions that it can and likely does have as dispositional parts include cultural competencies, interpersonal competencies, competencies for navigating a society's systems of laws, claims, obligations, deontic declarations, and norms of financial and other economic exchange.
The realization of this disposition by definition realizes the bearer's linguistic competence that is a dispositional part of this disposition. The realization of the linguistic competence would be an occurrent part of the realization of this disposition (and not a temporal part).
Whereas linguistic competence may be afforded to non-human agents, literacy is nearly always considered in the context of human beings.
linguistic literacy competence
A human social role that, if realized, is realized in providing assistance in the activities of daily living of another human being who possesses reduced capability to complete some of these activities alone.
John Judkins
caregiver role
A relational quality that inheres within two or more persons related as members of a domestic group, or a number of domestic groups linked through descent from a common ancestor, marriage, or adoption.
We are also intending on including other family arrangements. This is something we are working on.
family relationship
Examples of monetary forms of payment include: wages, salary, or tips; interest generated by capital; dividends earned; lottery, game, or contest monetary winnings; alimony; royalties; trusts; pensions; receipt of rental payments; unemployment payments; social security payments; worker's compensation; social security payments; or profit from entrepreneurial activities.
A data item that is about the sum of earnings for some person(s) from various forms of payment or profits.
We use the phrase ‘some person’ in the definition because this class can be about an individual's or a household's earnings. Similarly, we use 'personal income' in the label because the term is typically restricted to individuals and households. This class is also restricted to being about monetary forms of income.
monetary personal income data item
Taking notes on a meeting is an example in which the concretization relation is newly established, since the SDCs that concretize the GDCs come into existence as the notes are written. In contrast, using slides prepared by someone else in order to convey information during a presentation is a case of using a concretization in which the performer neither brings the concretizing SDCs into existence nor is responsible for their standing in the concretization relation to the relevant GDCs. A nonlinguistic example is drawing the logo of one’s favorite brand, in which one creates a pattern that concretizes a GDC that is also concretized by patterns on products of the brand.
Process in which some participant utilizes some specifically dependent continuant as a concretization of some generically dependent continuant.
Instances include any process that brings it about that some specifically dependent continuant begins to stand in a concretization relation to some generically dependent continuant, as well as any process in which someone makes use of a pre-established concretization relation. To be clear, instances do not include using concretizations of words or letters for purposes that do not make use of the concretization relations in which they stand (for example, hanging up a sign in a foreign language as a decoration because one likes the colors, despite having no idea what the sign says).
Instances include, but are not limited to, processes that bring about cognitive concretizations.
concretization-utilization process
A concretization-utilization process in which the utilized specifically dependent continuant concretizes the generically dependent through use of some language.
linguistic concretization-utilization process
For example, reading a text message that says, “It is raining outside,” and inferring that the words on the screen are meant to convey information about the weather. The pattern on the screen that corresponds to the words is the SDC, and the ICE about the rain is the GDC. Or, hearing your spouse say, “Can you come to the kitchen?” and then knowing that your spouse wants you to come to the kitchen. You have interpreted the patterns of the sound as concretizing a GDC about what your spouse wants. Or, seeing a drawing of a basketball player and inferring—perhaps incorrectly—that it is of Michael Jordan.
Process in which some participant infers that some particular specifically dependent continuant stands in the concretization relation to some particular generically dependent continuant.
The interpretation need not be accurate. It may even be the case that the specifically dependent continuant has not previously concretized anything.
concretization-interpretation process
A concretization-interpretation process in which the specifically dependent continuant is inferred to concretize the generically dependent continuant in a way that makes use of some language.
linguistic concretization-interpretation process
A disposition that inheres in some material entity and is such that that, if realized, it is realized by either some linguistic concretization-utilization process or some linguistic concretization-interpretation process.
When realized in a concretization-utilization process, the only relevant concretization may in some cases be a cognitive one, but that suffices to realize a linguistic competence. For example, suppose one begins to write a letter, planning out the words ahead of time, but is interrupted before beginning to write and never resumes. During the process of planning out the words and what one intends to communicate, one is already concretizing words cognitively, as well as considering which combinations of words one can use to concretize additional generically dependent continuants. In doing so, one performs processes that realize one's linguistic competence, without producing any concretizations other than those cognitive ones.
linguistic competence
A process in which some participant shares some generically dependent continuant with some other participant. The former utilizes some specifically dependent continuant that concretizes the generically dependent continuant intended to be shared, while the latter interprets that specifically dependent continuant to concretize some particular generically dependent continuant, aiming to accurately infer the other participant’s intent.
For example, if you tell someone, “It is raining,” you produce sounds that have patterns that concretize information about the weather. Your utilization of that concretization is part of the communication. When the other person hears you, they interpret those patterns to concretize something, which may or may not be the same as what you intended to convey. In other words, they interpret the sounds you produce to have meanings associated with them, and that interpretation process is another part of the communication. If a process does not have a part of each type, it is not a communication.
The interpretation need not correspond exactly to what was intended by the other participant.
communication
A disposition that (i) is an aggregate of linguistic competences, considered as forming a distinct group on the basis of perceived common characteristics, such as mutual intelligibility among their bearers, in addition to historical or cultural factors; (ii) if realized, is realized in any and all realizations of those linguistic competences; and (iii) inheres in a linguistic community.
language
A communication in which some participant states a preference for some communicative process to be in a certain language, via some concretization of some preferred language information content entity.
disclosure of preferred language
An information content entity that is about some person and some language, and that conveys the language with which that person prefers to communicate within some given context.
preferred language information content entity
A role that inheres in some entity that is realized in a social act.
role in human social processes
An information content entity that is the specified outcome of and documents the sucessful completion of a tertiary education program.
Recognized degree awarded after successful completion of a college or post-graduate porgram.
academic degree
An academic degree awarded by colleges and universities upon completion of a program of study lasting two years.
Recognition awarded after completion of a specific curriculum from an accredited tertiary education provider that falls between high school and bachelor's degree program.
associate degree
An academic degree awarded by universities upon completion of a course of study demonstrating a mastery or high-order overview of a specific field of study or area of professional practice.[1] Within the area studied, graduates are posited to possess advanced knowledge of a specialized body of theoretical and applied topics; high order skills in analysis, critical evaluation, or professional application; and the ability to solve complex problems and think rigorously and independently.
master's degree
An academic degree awarded by colleges and universities upon completion of a course of study lasting three to seven years.
bachelor's degree
An academic degree in the science and principles of nursing, granted by an accredited tertiary education provider after the successful completion of a bachelor's of nursing program.
bachelor's of nursing degree
An academic degree in the science and principles of nursing, granted by an accredited tertiary education provider after the successful completion of a master's of nursing program.
An advanced academic degree in the principles and practices of nursing, with a focus on administration, education, or advanced nursing practice, granted by an accredited college or university after the successful completion of a master's of nursing program.
master's in the science of nursing degree
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
A time quality inhering in a bearer by virtue of how long the bearer has existed.
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 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 biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
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.
quality of a single physical entity
A physical object quality which inheres in a single-bearer.
A quality which inheres in a continuant.
A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.
Needs axioms for family relationships.
Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry.
family
Faint is a alteration of consciousness characterized by a loss of consciousness because of a temporary decrease in the blood supply to the brain.
A symptom is a perceived change in function, sensation, loss, disturbance or appearance reported by a patient indicative of a disease.
A skin and integumentary tissue symptom characterized as an eruption on the body typically with little or no elevation above the surface.
Wheezing is a respiratory abnormality characterized by breathing with difficulty usually with a whistling sound.
Dizziness is a neurological and physiological symptom characterized by a sensation of unsteadiness accompanied by a feeling of movement within the head.
Fever is a neurological and physiological symptom characterized by a rise of body temperature above the normal whether a natural response (as to infection) or artificially induced for therapeutic reasons.
Low-grade fever is a fever that does not exceed 38.5 degree centrigrade.
High fever is a fever that involved an elevated temperature.
Vomiting is a digestive system symptom characterized by throwing up the stomach contents.
Dyspnea is a respiratory abnormality characterized by difficult or labored respiration.
First portion of the digestive tract[WP]. The portion of the digestive that develops from the stomodeum
TODO - check fly mouthpart. note in uberon we distinguish between the mouth and the oral opening. the mouth is part of the digestive tract. TODO - check isa parent subdivision of head - is it a subdivision of the head or digestive tract
Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]. Striated muscle tissue under control of the somatic nervous system. It is one of three major muscle types, the others being cardiac and smooth muscle. As its name suggests, most skeletal muscle is attached to bones by bundles of collagen fibers known as tendons. Skeletal muscle is made up of individual components known as muscle fibers. These fibers are formed from the fusion of developmental myoblasts. The myofibers are long, cylindrical, multinucleated cells composed of actin and myosin myofibrils repeated as a sarcomere, the basic functional unit of the cell and responsible for skeletal muscle's striated appearance and forming the basic machinery necessary for muscle contraction. The term muscle refers to multiple bundles of muscle fibers held together by connective tissue[WP].
TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Consider FBbt:00005073 - somatic muscle.
Organ with organ cavity which is continuous proximally with the right and left ureters and distally with the urethra.
editor note: consider adding a 'bladder' grouping class
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA].
Note that this class combines superficial fascia and hypodermis in FMA. Note also BTO has 'subcutis'
Nonparenchymatous organ that consists of the dermis and epidermis. Subdivisions of the skin surround various body parts; as a whole, the skin constitutes the external layer of the body. Examples: There is only one skin[FMA]. Surface structure that consists of the external membranous integument of the animal.
Note that FMA uses 'skin' for the entire organ. XAO seems consistent. MA seems to use it analagously to zone of skin
A vaccination informed consent form that is provided by Manitoba government in Canada
Manitoba vaccination informed consent form
a questionnaire that is part of the Manitoba vaccination informed consent form.
We may also model the Minatoba Child Informed Consent form: http://www.gov.mb.ca/health/publichealth/cdc/div/docs/7707.pdf
questionnaire for Manitoba vaccination consent
A questionnaire that contains different questions of an intended vaccine reciepiant's health history, allergy history, and current condition, in order to assess the contraindication and precaution for administering a vaccine.
YL,JZ,YH
vaccination screening questionnaire
a question textual entity that asks whether the questionee is allergic to a vaccine component
question whether allergic to vaccine component
don't know answer text entity
questionnaire for Rite Aid vaccination consent
a questionnaire for Costco vaccination consent that is filled
filled questionnaire for Costco vaccination consent
a questionnaire for Walgreens vaccination consent that is filled
filled questionnaire for Walgreens vaccination consent
questionnaire for Rite Aid vaccination consent in California
vaccination patient with asthma
questionnaire for Rite Aid injectable flu vaccination consent in South Carolina
questionnaire for Rite Aid non-flu vaccination consent in South Carolina
questionnaire for Rite Aid vaccination consent in other states than SC, NC and CA
a human who is going to recieve an administration of a vaccine, who bears a vaccination patient role, which is realized when he/she sits in a vaccination provider's site and is the bject of screening questions for receiving a vaccine.
After the vaccination process, this vaccination patient will bear the role of human vaccinee, and become a human vaccinee.
If the patient is a minor, his/her legal representative will answer the screening question for him/her.
vaccination patient
legal representative of minor vaccination patient
A vaccination informed consent form that is provided by Costco
Costco vaccination informed consent form
A vaccination informed consent form that is provided by Walgreens
Walgreens vaccination informed consent form
a questionnaire that is part of the Walgreens vaccination informed consent form.
questionnaire for Walgreens vaccination consent
a questionnaire that is part of the Costco vaccination informed consent form.
questionnaire for Costco vaccination consent
a vaccination patient who is under the age of legal competence.According to US Civil Law, which described a person under a certain age as less than so many years. In most states, a person is no longer a minor after reaching the age of 18.
minor vaccination patient
female vaccination patient
flumist vaccination
Rite Aid vaccination informed consent form
pneumococcal vaccination
Zoster vaccination
shingles vaccination
Tdap vaccination
vaccination patient over 65 years old
questionnaire for Rite Aid vaccination consent in North Carolina
Td vaccination
vaccination patient with COPD
vaccination patient with smoking habit
2-4 year old vaccination patient
parent of minor vaccination patient
influenza vaccination
injectable influenza vaccination
intranasal influenza vaccination
Rite Aid injectable flu vaccination informed consent form in South Carolina
Rite Aid non-flu vaccination informed consent form in South Carolina
Rite Aid vaccination informed consent form in California
Rite Aid vaccination informed consent form in North Carolina
Rite Aid vaccination informed consent form in other states than SC, NC and CA
Manitoba Seasonal Influenza and Pneumococcal vaccination informed consent form
Manitoba child immunization consent form
questionnaire for Manitoba child immunization consent
yellow fever vaccination
MMR vaccination
typhoid vaccination
oral typhoid vaccination
live vaccine vaccination
University of Maryland College Park vaccination informed consent form
questionnaire for University of Maryland College Park vaccination consent
UM College Park injectable influenza vaccination informed consent
UM College Park flumist vaccination informed consent
UM College Park Smallpox vaccination informed consent form
questionnaire for UM College Park flumist vaccination consent
questionnaire for UM College Park injectable influenza vaccination consent
screening questionnaire for UM College Park smallpox vaccination consent
smallpox vaccination
a person lives in the same house with vaccination patient
household member of vaccination patient
a person who has close physical contact with the vaccination patient, such as sex partner
close physical contact person of vaccination patient
A newborn infant, or neonate, is a child under 28 days of age.
WHO (http://www.who.int/topics/infant_newborn/en/)
NCI: C16731
newborn infant
vaccination informed consent process
a question textual entity that asks whether the questionee is currently sick.
Are you sick today
1. Are you sick today? There is no evidence that acute illness reduces vaccine efficacy or increases vaccine adverse events (1). However, as a precaution with moderate or severe acute illness, all vaccines should be delayed until the illness has improved. Mild illnesses (such as upper respiratory infections or diarrhea) are NOT contraindications to vaccination. Do not withhold vaccination if a person is taking antibiotics. (http://www.immunize.org/catg.d/p4065.pdf)
question whether currently sick
a question textual entity that asks whether the questionee is allergic to some material.
2. Do you have allergies to medications, food, a vaccine component, or latex? If a person has anaphylaxis after eating gelatin, do not administer MMR,varicella, standard trivalent Fluzone, Flumist, rabies (Rabavert), oral typhoid, or yellow fever vaccine. A local reaction to a prior vaccine dose or vaccine components (e.g., latex) is not a contraindication to a subsequent dose or vaccine containing that component. For a table of vaccines supplied in vials or syringes that contain latex, go to www.cdc.gov/vaccines/pubs/pinkbook/downloads/appendices/B/latex-table.pdf. For an extensive list of vaccine components, see reference 2. An egg-free recombinant influenza vaccine (RIV3) may be used in people age 18 years and older with egg allergy of any severity who have no other contraindications. People younger than age 18 years who have experienced a serious systemic or anaphylactic reaction (e.g., hives, swelling of the lips or tongue, acute respiratory distress, or collapse) after eating eggs can usually be vaccinated with inactivated influenza vaccine (IIV); consult ACIP recommendations (see reference 3). 2. Table of Vaccine Components: www.cdc.gov/vaccines/pubs/pinkbook/downloads/appendices/B/excipient-table-2.pdf. 3. CDC. Prevention and control of influenza with vaccines:Recommendations of the Advisory Committee on Immunization Practices (ACIP), United States, 2015–16 Influenza Season at www.cdc.gov/mmwr/pdf/wk/mm6430.pdf, pages 818–825 http://www.immunize.org/catg.d/p4065.pdf
allergy question
a question textual entity that asks whether the questionee is allergic to latex.
question whether allergic to latex
a question textual entity that asks whether the questionee is allergic to food
question whether allergic to food
question whether allergic to egg
a question textual entity that asks whether the questionee is allergic to a medication
question whether allergic to medication
a question textual entity that asks whether the questionee is allergic to a vaccine
question whether allergic to vaccine
a question textual entity that asks whether the questionee had any reaction after a vaccination (i.e., immunization) in the past.
question on reaction after immunization
a question textual entity that asks whether the questionee has experienced any seizure disorder
seizure disorder question
a question textual entity that asks whether the vaccination patient is immunocomprised
immunocompromisation question
a question textual entity that asks whether a woman is pregnant now
question on woman pregnancy
a question textual entity that asks whether the questionee is currently under any treatment
current treatment question
a current treatment question that asks whether the questionee is currently under any cortisone treatment
cortisone treatment question
a current treatment question that asks whether the questionee is currently under any X-ray treatment
X-ray treatment question
a question textual entity that asks whether the questionee has been vaccinated in the past four weeks
question on vaccination in past 4 weeks
a question textual entity that asks whether the questionee has conducted a TB skin test in the past four weeks
question on TB skin test in past 4 weeks
a question textual entity that asks whether the questionee has conducted a blood transfusion in the past year
question on blood transfusion in past year
a current treatment question that asks whether the questionee has been under a high-dose steroid therapy ((prednisone > 20mg/day or equivalent)) for longer than two weeks
question on high-dose steroid therapy for longer than 2 weeks
a question textual entity that asks whether the questionee has a thymus disease
This question is needed for yellow fever vaccination
question on thymus disease
a question textual entity that asks whether the questionee is currently taking some antibiotics
This question is needed for oral typhoid vaccination
question on current antibiotics usage
a question textual entity that asks whether the questionee has a history of thrombocytopenia
question on thrombocytopenia history
a question textual entity that asks whether the questionee is currently taking aspirin
question on current aspirin medication
a question textual entity that asks whether the questionee has a history of asthma or wheezing
question on asthma or wheezing history
a question textual entity that asks whether the questionee has a serious nasal condition, which makes breathing difficult, such as a very stuffy nose.
question on serious nasal condition
a question textual entity that asks whether the questionee has a a long-term health problem with heart disease, lung disease, asthma, kidney disease, metabolic disease (e.g., diabetes), anemia or other blood disorder.
question on long-term health problem
a question on long-term health problem that asks whether the questionee has a long-term heart disease
question on long-term heart disease
a question on long-term health problem that asks whether the questionee has cancer
question on cancer
a question on long-term health problem that asks whether the questionee has leukemia
question on leukemia
a question on long-term health problem that asks whether the questionee has a long-term lung disease
YL, YH
question on long-term lung disease
YL,YH
filled questionnaire for Manitoba Seasonal Influenza and Pheumococcal vaccination consent
a question on long-term health problem that asks whether the questionee has a long-term metabolic disease
question on long-term metabolic disease
a question on long-term health problem that asks whether the questionee has diabetes
question on long-term diabetes
a question on long-term health problem that asks whether the questionee has anemia
question on anemia
a question on long-term health problem that asks whether the questionee has AIDS
question on AIDS
a current treatment question that asks whether the questionee is currently under prednisone treatment
prednisone treatment question
a current treatment question that asks whether the questionee is currently under any steroid treatment
steroids treatment question
a question textual entity that asks whether the questionee is currently taking any anti-cancer drugs
question on current anti-cancer drug usage
Walgreens immunization informed consent: https://www.walgreens.com/images/pdfs/IN-2225/WAG_VAR_Form_EDIT_10172013_v1.pdf
a question textual entity that asks whether the questionee hasfainted or felt dizzy after a vaccination (i.e., immunization)
question on whether fainted or felt dizzy after immunization
a question textual entity that asks whether the questionee has been given transfusion of blood products in the past year
question on transfusion of blood products in past year
a question textual entity that asks whether the questionee has been given immune (gamma) globulin in the past year
question on given immune (gamma) globulin in last year
a question textual entity that asks whether the questionee has a history of thymoma
question on history of thymoma
a question textual entity that asks whether the questionee has his/her thymus removed previously
question on previous thymectomy procedure
a question textual entity that asks whether the questionee is currently under antimalarial medication
asked in prior for using Oral thyphoid vaccine only
question on current antimalarial medication
a question textual entity that asks whether the questionee has experienced any seizure disorder, brain or nerve problem.
Have you had a seizure, brain, or other nervous system problem?
question on seizure, brain, or nerve problem
Cosco Pharmacy vaccine informed consent form: http://www2.costco.com/Images/Content/misc/PDF/Immunization_consent_form_v2-2012.pdf
a question textual entity that asks whether the questionee has conducted a blood or blood product transfusion, or given a medicine called immune (gamma) globulin, in the past year
During the past year, have you received a transfusion of blood or blood products, including antibodies?
question on blood or blood product transfusion, or immune (gamma) globulin in past year
a question textual entity that asks whether a woman is pregnant now or could become pregrant during the next month
question on woman pregnancy now or during the next month
a question textual entity that asks whether the questionee has cancer, leukemia, AIDS or any other immune system problem
question on cancer, leukemia, AIDS or any other immune system problem
a question textual entity that asks whether the questionee is currently sick with a moderate to high fever, vomiting/diarrhea
question whether currently sick with a moderate to high fever, vomiting/diarrhea
a question textual entity that asks whether the questionee has taken any medication that affects blood clotting
question on any medication affecting blood clotting
a question textual entity that asks whether the questionee has a history of thrombocytopenia or thrombocytopenic purpura.
question on history of thrombocytopenia or thrombocytopenic purpura
a questionnaire that is part of the vaccination informed consent form used for Seasonal Influenza and Phenumococcal vaccination in Manitoba, Canada.
questionare for Manitoba Seasonal Influenza and Pneumococcal vaccination consent
a question on long-term health problem that asks whether the questionee has a long-term kidney disease
question on long-term kidney disease
question whether allergic to gentamicin
question whether allergic to neomycin
question whether allergic to formaldehyde
question whether allergic to thimerosal
question whether allergic to bovine protein
question whether allergic to phenol
question whether allergic to polymyxin
question whether allergic to gelatin
question whether allergic to yeast
question whether allergic to baker’s yeast
question on vaccination caused disorder
question on vaccination caused Guillain-Barre syndrome
question on neurological disorder
a question asks the questionee if he or she is taking care of a new born infant or close family member of a new born infant.
Are you a parent, family member, or caregiver to a new born infant?
question whether relate to new born infant
question on asthma history
question on wheezing history
question on serious reaction after immunization
question whether a parent of a new born infant
question whether a family member of a new born infant
question whether a care giver of a new born infant
Do you smoke?
question whether smoke
questions that related to patient's vaccination history, warnings received from health provider about a certain vaccination, and adverse event related with a vaccination.
question on past vaccination information
question whether had Pneumococcal vaccination
question whether had Shingles vaccination
question whether had Tdap vaccination
question on antiviral drug usage
Do you have a cut, injury, puncture or open wound that prompted you to get a tetanus shot?
question on whether having cut, injury, puncture or open wound
question on COPD
question whether react to triple antibiotic ointment
Has any physician or other healthcare professional ever cautioned or warned you about receiving certain vaccines or receiving vaccines outside of a medical setting? *
a question asks if the vaccination patient received warning or precaution information from his/her health provider in the past.
question on health provider precaution or warning of specific vaccination
question about vaccination patient age
question on long-term liver disease
question on faintig after vaccination
question on long-term aspirin therapy
Are you 18 years of age or older?
question whether patient is older than 18 years old
question on whether having atopic dermatitis
question whether diagnosed with rheumatoid arthritis
question whether diagnosed with ankylosing spondylitis
question whether diagnosed with Crohn’s disease
Have you ever been diagnosed as having Guillain-Barre syndrome?
question whether diagnosed with Guillain-Barre syndrome
question on health condition requires doctor visit
a question textual entity that asks the patient whether he/she had diagnosed, treated and recovered from chickenpox, or varicella-zoster virus (VZV) infection.
question whether had chickenpox
question on dizzy after vaccination
Did you bring your Immunization Record Card with you?
question whether bring imunization record card
question on asplenia
question on CSF leak
The United States Food and Drug Administration reports that cochlear implant recipients may be at higher risk for meningitis.[76] A study of 4,265 American children who received implants between 1997 and 2002 concluded that recipient children had a risk of pneumococcal meningitis more than 30 times greater than that for children in the general population.A later, UK-based, study found that while the incidence of meningitis in implanted adults was significantly higher than the general population, the incidence in children was no different from the general population. As a result, the Centers for Disease Control and Prevention and the Food and Drug Administration both recommend that would-be implant recipients be vaccinated against meningitis prior to surgery.(https://en.wikipedia.org/wiki/Cochlear_implant)
question on cochlear implant
question on weekly injection
question on weekly injection of adalmumab
question on weekly injection of infliximab
question on weekly injection of etanercept
question on home infusion
question on high-dose methotrexate usage
question on azathioprine or 6-mercaptopurine usage
question on current anti-malarial medication
question whether recieving aspirin-containing therapy
a minor vaccination patient whose age is younger thatn 5 or equal to 5.
5 year and younger vaccination patient
Do you have a fever?
question on fever
question whether allergic to egg products
question on stroke leading brain or nerve damage
question on convulsion leading brain or nerve damage
question on brain or nerve damage
question that is about the patient's repiratory system or chest symptoms.
question on respiratory illness
question whether in contact with severely immunocompromised person
Is there a possibility of pregnancy? <used in UM College Park injectable influenza vaccination consent questionnaire> [VICO_0000065]
Pregnancy tests prior to vaccination are not routinely recommended. However, females of childbearing age should be asked about the possibility of their being pregnant prior to being given any vaccine for which pregnancy is a contraindication or precaution. The patient's answer should be documented in the medical record. If the patient is uncertain if she is pregnant, a test should be performed before administering live virus vaccines (measles-mumps-rubella, varicella, live attenuated influenza, yellow fever). (http://www.immunize.org/askexperts/precautions-contraindications.asp)
question on woman's possibility of geting pregnant
question on agammaglobulinemia
question on lymphoma
question on severe autoimmune disease
question on SLE
question on immunosuppressive drug usage
question on drug usage after organ transplant
question on autoimmune disease drug usage
question on cancer treatment
question on autoimmune disease
question on current condition leads to skin break
question onwhether having skin rash
question on whethere having severe burn
question on whether having impetigo
question whether having chickenpox
question on whether having shingles
question on whether having herpes
question on whether having psoriasis
question on whether having severe acne
question on Darier's disease
question on whether using steroid eye drop
question on whether diagnosed with myocardial infarction
question on whether diagnosed with angina
question on whether diagnosed with congestive heart failure
question on whether diagnosed with cardiomyopathy
question on whether had transient ischemic attack
question on chest pain
question on shortness of breath when exert
question whether allergic to smallpox vaccine
question whether allergic to polymixin B
question whether allergic to streptomycin
question whethere allergic to chlortetracycline
question whethere allergic to neomycin
question on last month's sexual intercourse without effecctive birth control
question on sexual intercourse without effecctive birth control after the vaccination
question whether live with a child less than one year old
question whether current breast-feeding
CDC guidance for pregnancy vaccination http://www.cdc.gov/vaccines/acip/committee/downloads/preg-principles-2008.pdf
question for woman
question for household memeber of vaccination patient
question for close physical contact person of vaccination patient
question asks vaccination patient about current drug usage.
question on current medication usage
question whether had organ transplant
question whether had chickenpox vaccination
a question asks if the patient currently has any disease that requies regular doctor's vsisit, long tem disease that impacts current well-being, any symptoms, or feeling ill at the time when he/she is being accessed by vaccination providers.
current health condition question
previous medical precedure question
question whether live with immunocompromise person
A disposition of ill health, bodily malfunction, or discomfort.
sickness
A condition or state in which the immune system doesn't have ability to fight infectious disease or medical challenges.
A person who has an immunodeficiency of any kind is said to be immunocompromised. An immunocompromised person may be particularly vulnerable to opportunistic infections, in addition to normal infections that could affect everyone. Immunodeficiency may also decrease cancer immunosurveillance. Most cases of immunodeficiency are acquired ("secondary") but some people are born with defects in their immune system, or primary immunodeficiency. Transplant patients take medications to suppress their immune system as an anti-rejection measure, as do some patients suffering from an over-active immune system.
immunocompromised condition
The organism's spleen doesn't work, or
functional asplenia
The organsim is lacking of the spleen as a part of its body.
anatomical asplenia
Asplenia refers to the absence of normal spleen function and is associated with some serious infection risks.
Asplenia refers to the absence of normal spleen function and is associated with some serious infection risks.Asplenia is a form of immunodeficiency, increasing the risk of sepsis from polysaccharide encapsulated bacteria,and can result in overwhelming post splenectomy infection (OPSI), often fatal within a few hours. In particular, patients are at risk from Streptococcus pneumoniae, Haemophilus influenzae, and meningococcus.The risk is elevated as much as 350–fold. (https://en.wikipedia.org/wiki/Asplenia)
Vaccinations It is suggested that splenectomized persons receive the following vaccinations, and ideally prior to planned splenectomy surgery: Pneumococcal polysaccharide vaccine (not before 2 years of age). Children may first need one or more boosters of pneumococcal conjugate vaccine if they did not complete the full childhood series. Haemophilus influenzae type b vaccine, especially if not received in childhood. For adults who have not been previously vaccinated, two doses given two months apart was advised in the new 2006 UK vaccination guidelines (in the UK may be given as a combined Hib/MenC vaccine). Meningococcal conjugate vaccine, especially if not received in adolescence. Previously vaccinated adults require a single booster and non-immunised adults advised, in UK since 2006, to have two doses given two months apart. Children too young for the conjugate vaccine should receive meningococcal polysaccharide vaccine in the interim. Influenza vaccine, every winter, to help prevent getting secondary bacterial infection. (https://en.wikipedia.org/wiki/Asplenia)
asplenia
The immunocomproised condition accquired by transplant patients taking medications to suppress their immune system as an anti-rejection measure.
acquired immunocompromised condition due to transplant
A health condition where the fluid surrounding the brain and spinal cord escapes.
CSF leak
cerebrospinal fluid leak
a condition of person who has been surgically implanted an electronic device under the skin behind the ear to provide hearing.
The United States Food and Drug Administration reports that cochlear implant recipients may be at higher risk for meningitis.[76] A study of 4,265 American children who received implants between 1997 and 2002 concluded that recipient children had a risk of pneumococcal meningitis more than 30 times greater than that for children in the general population.[77] A later, UK-based, study found that while the incidence of meningitis in implanted adults was significantly higher than the general population, the incidence in children was no different from the general population.[78] As a result, the Centers for Disease Control and Prevention and the Food and Drug Administration both recommend that would-be implant recipients be vaccinated against meningitis prior to surgery.[79]
cochlear implant
serious vaccine adverse event
The state or condition of having a developing embryo or fetus in the body (uterus), after union of an ovum and spermatozoon, during the period from conception to birth.
pregancy
A burn is an injury to the skin or other organic tissue primarily caused by heat or due to radiation, radioactivity, electricity, friction or contact with chemicals. Skin injuries due to ultraviolet radiation, radioactivity, electricity or chemicals, as well as respiratory damage resulting from smoke inhalation, are also considered to be burns.
WHO (http://www.who.int/violence_injury_prevention/other_injury/burns/en/)
burns
The feeding of babies and young children with milk from a woman's breast.
breastfeeding
A person's current tobacco and nicotine consumption as well as his/her smoking history.
smoking behaviour
Sexual intercourse without the use of precautions to prevent conception or the transmission of sexually transmitted diseases.
NCI thesaurus
unprotected sexual intercourse
'part of organism in vaccine' is a pathogen component in vaccine that contains only a part of the pathogen organism instead of the whole organism.
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 process of administering substance in vivo that involves in adding a vaccine into a host (e.g., human) in vivo with the intent to invoke a protective or therapeutic adaptive immune response.
Product Name: Haemophilus b Conjugate Vaccine (Tetanus Toxoid Conjugate)
Product Name: Tetanus Toxoid, Reduced Diphtheria Toxoid and Acellular Pertussis Vaccine, Adsorbed
WEB: http://www.cdc.gov/vaccines/pubs/pinkbook/downloads/appendices/B/excipient-table-2.pdf
Product Name: Measles Virus Vaccine, Live
A vaccine that protects against Bacillus anthrax that causes anthrax.
Product Name: Haemophilus b Conjugate Vaccine (Meningococcal Protein Conjugate) & Hepatitis B Vaccine (Recombinant)
Vaccine components see http://www.vaccinesafety.edu/components-DTaP.htm
Product Name: Diphtheria & Tetanus Toxoids & Acellular Pertussis Vaccine Adsorbed
Product Name: Tetanus & Diphtheria Toxoids Adsorbed for Adult Use
Product Name: Diphtheria & Tetanus Toxoids Adsorbed
Diphtheria and Tetanus Toxoids Adsorbed USP by Sanofi Pasteur Inc
Diphtheria and Tetanus Toxoids Adsorbed by Sanofi Pasteur Ltd
a vaccinia virus vaccine that is a freeze-dried calf lymph smallpox vaccine, specifically, Dryvax is a live-virus preparation of vaccinia prepared from calf lymph.
Dryvax is a freeze-dried calf lymph smallpox vaccine. It is the world's oldest smallpox vaccine, created in the late 19th century by American Home Products, a predecessor of Wyeth. By the 1940s, Wyeth was the leading US manufacturer of the vaccine and the only manufacturer by the 1960s. After world health authorities declared smallpox had been eradicated from nature in 1980, Wyeth stopped making the vaccine.
Product Name: Smallpox Vaccine, Dried, Calf Lymph Type
Product Name: Influenza Virus Vaccine, Trivalent, Types A and B
Product Name: Influenza Virus Vaccine, Live, Intranasal
Product Name: Human Papillomavirus (Types 6, 11, 16, 18) Recombinant Vaccine
Product Name: Hepatitis A Vaccine, Inactivated
A bacterial vaccine that prevents Neisseria meningitidis infection.
Product Name: Poliovirus Vaccine Inactivated (Monkey Kidney Cell)
WEB: http://atomicnewsreview.org/2009/10/22/approval-for-the-arepanrix%E2%84%A2-gsk-vaccine-in-canada/
Product Name: Influenza Virus Vaccine, H5N1 (for National Stockpile)
Influenza Virus Vaccine H5N1 (Sanofi Pasteur Inc)
Product Name: Japanese Encephalitis Virus Vaccine Inactivated
Product Name: Diphtheria and Tetanus Toxoids and Acellular Pertussis Adsorbed and Inactivated Poliovirus Vaccine
A Measles-Mumps-Rubella vaccine that is live attenuated and manufactured by Merck & Co, Inc.
Product Name: Measles, Mumps, and Rubella Virus Vaccine, Live
A Measles-Mumps vaccine that is manufactured by Merck and used for human.
Product Name: Measles and Mumps Virus Vaccine, Live
Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugate Vaccine
WEB: http://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm176044.htm
Product Name: Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugate Vaccine
Product Name: Meningococcal Polysaccharide Vaccine, Groups A, C, Y and W-135 Combined
Product Name: Rubella Virus Vaccine Live
an influenza vaccine that is similar to Fluzone but has high dose.
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM305079.pdf
Fluzone High-dose
Influenza A (H1N1) 2009 Monovalent Vaccine (Novartis)
Product Name: Diphtheria & Tetanus Toxoids & Acellular Pertussis Vaccine Adsorbed, Hepatitis B (recombinant) and Inactivated Poliovirus Vaccine Combined
Product Name: Haemophilus b Conjugate Vaccine (Meningococcal Protein Conjugate)
Product Name: Diphtheria and Tetanus Toxoids and Acellular Pertussis Adsorbed, Inactivated Poliovirus and Haemophilus b Conjugate (Tetanus Toxoid Conjugate) Vaccine
Plague Vaccine by Greer Laboratories Inc
Product Name: Pneumococcal Vaccine, Polyvalent
Product Name: Poliovirus Vaccine Inactivated (Human Diploid Cell)
Product Name: Pneumococcal 7-valent Conjugate Vaccine (Diphtheria CRM197 Protein)
A Measles-Mumps-Rubella-Vericella vaccine that is live and manufactured by Merck & Co, Inc.
WEB: http://www.merck.com/product/usa/pi_circulars/p/proquad/proquad_pi.pdf
Product Name: Measles, Mumps, Rubella and Varicella Virus Vaccine Live
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM305080.pdf
Fluzone intradermal
Product Name: Rotavirus Vaccine, Live, Oral, Pentavalent
Intravesical TICE BCG has been used as a therapy for, and to prevent recurrence of, tumors in patients with carcinoma in situ (CIS) of the urinary bladder, and to prevent recurrence of Stage Ta T1 papillary tumors of the bladder at high risk of recurrence. Refernce URL: http://www.ticebcg.com/Consumer/aboutTice/index.asp
Product Name: Typhoid Vi Polysaccharide Vaccine
Tetanus Toxoid Adsorbed by Aventis Pasteur Inc
Tetanus and Diphtheria Toxoids Adsorbed by MA Biologic Lab
Product Name: Hepatitis A Inactivated and Hepatitis B (Recombinant) Vaccine
Product Name: Varicella Virus Vaccine Live
Product Name: Typhoid Vaccine Live Oral Ty21a
A viral vaccine that protects against infection with Yellow fever virus.
Product Name: Zoster Vaccine, Live, (Oka/Merck)
an adjuvant role that inheres in a vaccine component which is added as part of a vaccine and induces enhanced adaptive immune response to the vaccine antigen.
Influenza A (H1N1) 2009 Monovalent Vaccine (Sanofi Pasteur)
A vaccine that targets against a bacterial disease.
a virulence of vaccine organism that shows an attenuated pheontype of the organism as the major component of a vaccine.
A vaccine that prevents or treats cancer. It is produced using the patient's own whole tumor cells as the source of antigens, or using tumor-specific antigens, often recombinantly produced.
a processed material that is output of the vaccine preparation and part of a vaccine.
an organismal quality of a whole organism vaccine where the whole organism is inactivated/killed and lacks the capability of replication.
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.
a route of administration that inject the material(such as vaccines, allergens) directly into a muscle.
rounte of administration that located in nose.
Influenza A (H1N1) 2009 Monovalent Vaccine (CSL Limited)
Page 73, Chapter 6, Vaccine, 5th Edition. EXPERT CONSULT by Plotkin SA., et. al. 2008
a role inheres in a material entity, that has been added into a vaccine's formulation by the manufacture for a specific purpose. For example: adjuvant to enhance the effect of immunogen, perservatives, stablizers and those materials added for affecting PH and isotonicity.
Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugate Vaccine injection 0.5mL vial
Product Name: Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugate Vaccine injection 0.5mL vial
a Varicella-zoster virus vaccine that is live attenuated.
a pneumococcal vaccine that is formed using polyvalent polysaccharides
WEB: http://www.who.int/vaccines/en/pneumococcus.shtml
The most common form of the polyvalent pneumococcal vaccine is called the protein-polysaccharide combinations which is known as conjugate vaccines and contain 7–11 selected polysaccharides bound to a protein carrier. The protein-polysaccharide combinations are able to induce a T-cell dependent immune response. These vaccines are likely to be protective even in children under two years of age, and may reduce pneumococcal transmission through a herd effect.
WEB: http://en.wikipedia.org/wiki/Vaccinia
a Smallpox virus vaccine that uses vaccinia virus
Vaccinia virus is well known for its role as a vaccine that helped eradicate the smallpox disease, making it the first human disease to be successfully eradicated by science.
preventive vaccine function is a vaccine function realized by the process of vaccination and leading to induction of an adaptive immune response to the antigens in a vaccine, which protects against a specific disorder.
protein of pathogen organism as vaccine component
a chicken egg protein allergen where the protein allergen is ovalbumin, the main protein found in egg write, making up 60-65% of the total protein.
WEB: http://en.wikipedia.org/wiki/Ovalbumin
chicken ovalbumin egg protein allergen
a S. typhi vaccine that is live and orally administerred
typhoid live oral vaccine
Active immunization is an immunization process that entails the introduction of a foreign molecule into the body, which causes the body itself to generate adaptive immunity against the target.
WEB: http://en.wikipedia.org/wiki/Immunization
artificial active immunization is an active immunization that occurs when a person or animal is vaccinated with a specific vaccine.
induction of adaptive immune response to antigen is an active immunization process that results in induction of adaptive immune response to some antigens, for example, in a vaccine.
induction of adaptive immune response to antigen
disorder prevention is a processual entity that prevents a disorder that is the physical basis of a disease.
disorder treatment is a processual entity that leads to treat a disorder that is the physical basis of a disease.
modification of adaptive immune response to antigen is an active immunization process that results in modification of an adaptive immune response to some antigens, for example, in a therapeutic vaccine.
modification of adaptive immune response to antigen
a route of administration that is loacted in the hypodermis (subcutaneous tissue) region.
a human who has been administrated a vaccine
The therapeutic vaccine function is a function realized by the process of vaccination and leading to induction of an adaptive immune response to the antigens in a vaccine, which ameliorates a specific disorder.
a path that is located in gross anatomical part of an organism (e.g., human) and is used for administering a vaccine, a drug, fluid, poison, or other substance into the body.
CDISC has a codelist: Rout of Administration. Desription from CDISC: The course by which a substance was administered in order to reach the site of action in the body. CDISC_SDTM_Route_of_Administration_Terminology
vaccine preservative that has thimerosal as part.
H1N1 Influenza vaccine is an Influenza virus vaccine that is used to vaccinate against H1N1 Influenza subtype vaccine.
a vaccine component that is chemical substance added to vaccine and enhance and direct immune response to protective antigen. Many of vaccine adjuvants cause a range of serious side-effects.
immunization objective is the specification of an objective to achieve immunization.
vaccine preparation is a manufacturing process to produce a vaccine.
A vaccine that targets against a viral disease.
a role that inheres in a prepared material entity that is designed to induce protection or treatment for a disease or infection.
vaccine role
a role that inheres in a material entity that becomes an ingredient of a vaccine.
vaccine component role
a vaccine role that indicates the vaccine being a conjugate vaccine.
conjugate vaccine role
licensed vaccine role is a regulation-assigned role that indicates that a vaccine obtains official approval for commercial production and selling on the market.
A bacterial vaccine that protects against infection with Clostridium spp.
a Clostridium vaccine that protects against infection with Clostridium tetani that causes tenanus.
A viral vaccine that protects against infection with influenza virus.
A viral vaccine that protects against infection with Hepatitis B virus.
A viral vaccine that protects against infection with Hepatitis A virus.
A bacteria vaccine that prevents against Yersinia pestis infection that causes plague.
A viral vaccine that protects against infection with Rabies virus.
A viral vaccine that protects against infection with Smallpox virus.
A viral vaccine that protects against infection with Measles virus.
A viral vaccine that protects against infection with Rotavirus.
A bacterial vaccine that protects against infection with Haemophilus.
Haemophilus influenzae serotype b vaccine
A viral vaccine that protects against infection with Poliovirus.
A viral vaccine that protects against infection with Japanese encephalitis virus.
a vaccine against human papillomavirus infection
a Herpesvirus vaccine that is used against Varicella-zoster virus infection.
a Salmonella vaccine against typhoid fever (or called typoid), caused by Salmonella enterica enterica, serovar Typhi.
a Streptococcal vaccine that is used against S. pneumoniae infection, which causes pneumococcal diseases.
A Measles-Mumps vaccine that also protects against infection with Rubella virus.
A Corynebacterium diphtheriae vaccine that also protect against infection with Clostridium tetani.
A bacterial vaccine that protects against infection with Corynebacterium diphtheriae that causes Diphtheria.
A Measles virus vaccine that also protects against infection with Mumps virus.
A Measles-Mumps-Rubella vaccine that also protects against Vericella.
Diphtheria-Tetanus-Pertussis-Poliovirus vaccine
Diphtheria-Tetanus-Pertussis-Poliovirus-Hepatitis B vaccine
Diphtheria-Tetanus-Pertussis-Poliovirus-Haemophilus b vaccine
a viral vaccine against Hepatitis B virus and at the same time against bacterial H. influenzae serotype b.
A bacterial vaccine that prevents infection with Vibrio cholera.
BCG Vaccine is a Mycobacterium tuberculosis vaccine that is a live attenuated strain of Mycobacterium bovis (Bacillus Calmette Guerin; BCG).
a licensed vaccine role that indicates the vaccine occurs in USA.
a vaccine additive that helps to protect the vaccine from adverse conditions such as the freeze-drying process (for those vaccines that are freeze-dried) or heat.
Finn TM and Egan W, in Vaccines fifth edition, 2008. Page 75.
a vaccine residual that is generatead from cell culture for vaccine preparation. Examples include: antibiotics, sensitizing substances, bacterial and cellular residuals, and adventitious agents.
Finn TM and Egan W, in Vaccines fifth edition, 2008. Page 78-81.
a licensed status that occurs in Canada.
Influvac is an Influenza virus vaccine that is manufactured by Solvay Pharma.
Vaxigrip is an Influenza virus vaccine that is manufactured by 'Sanofi Pasteur Limited.
a mineral salt vaccine adjuvant that is composed of aluminum salt.
Aluminum vaccine adjuvant is a vaccine adjuvant that is composed of some aluminum compound.
a role inhers in a vaccine component that when added into a vccine formmulation, it can prevent the growth of bacteria or fungi that inadvertently may be introduced into the vaccine during administrating process or the manufacturing process.
P73 Chapter 6, Vaccine 5th edition by Plotkin, S. et al.
The CFR requires that, with certain defined exceptions, preservatives must be added to mulitdose vials of vaccine. (P73 Chapter 6, Vaccine 5th edition by Plotkin, S. et al.)
a route of administration that located in the mouth
a route of administration that inject the material(such as vaccines, allergens) into the skin itself.
vaccine allergen is a material entity that is capable of stimulating a type-I hypersensitivity reaction in atopic individuals who has been vaccinated with a vaccine.
a cell culture residual in vaccine that is bovine albumin.
bovine albumin cell culture residual in vaccine
a cell culture residual in vaccine that is bovine serum.
bovine serum cell culture residual in vaccine
a vaccine stablizer that is based on monosodium glutamate.
a cell culture residual in vaccine that is human albumin.
human albumin cell culture residual in vaccine
a cell culture residual in vaccine that is human serum.
human serum cell culture residual in vaccine
a vaccine stabilizer that is a polysorbate 20. It encourages the suspension of one liquid in another and has mild toxicity.
Potential Acute Health Effects: Slightly hazardous in case of skin contact (irritant), of eye contact (irritant), of ingestion, of inhalation. Reference: http://www.sciencelab.com/msds.php?msdsId=9926640
a vaccine emulsifier that uses polysorbate 80, also known as polyoxyethylene sorbitan monooleate or Tween™ 80.
WEB: http://www.wisegeek.org/what-is-polysorbate-80.htm
Tween 80 is an amber-colored, viscous liquid with a slightly bitter taste. The product is a derivative of sorbitol and oleic acid.
a cell culture residual in vaccine that is residual protein from cell culture.
vaccine residual protein from cell culture
a vaccine stabilizer that is specifically made by sorbitol.
Sorbitol, also known as glucitol, is a sugar alcohol that the human body metabolizes slowly. It can be obtained by reduction of glucose, changing the aldehyde group to a hydroxyl group. Sorbitol is found in apples, pears, peaches, and prunes. It is synthesized by sorbitol-6-phosphate dehydrogenase, and converted to fructose by succinate dehydrogenase and sorbitol dehydrogenase. Succinate dehydrogenase is an enzyme complex that participates in the citric acid cycle. (wikipedia)
a cell culture residual in vaccine that is sucrose albumin.
sucrose albumin cell culture residual in vaccine
a cell culture residual in vaccine that is from yeast extract.
yeast extract cell culture residual in vaccine
a cell culture residual in vaccine that is yeast protein.
yeast protein cell culture residual in vaccine
Diphtheria-Tetanus-Pertussis-Haemophilus b vaccine
A Measles virus vaccine that is also used against Rubella virus infection.
Diphtheria-Tetanus-Pertussis-Poliovirus-Haemophilus b-Hepatitis B vaccine
Flublok
Flucelvax
FluMist Quadrivalent
a tetanus vaccine manusfactured by Sanofi Pasteur Inc. that is only for booster use (not recommended for primary immunization)
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142732.pdf
Tetanus Toxoid (for Boost use Only) by Sanofi Pasteur Inc
a live attenuated quality of a bacterial vaccine strain.
bacterial vaccine organism live attenuated
a live attenuated quality of a virus vaccine strain.
viral vaccine organism live attenuated
a vaccination that occurs in the intramuscular route.
capsular polysaccharide of pathogen organism as vaccine component
a role of host that contains vaccine. It is a role that inheres in an organism that is the target of a vaccine administration (vaccination process).
The objective that intends to produce vaccine via the vaccine preparation process.
Influenza A (H1N1) 2009 Monovalent Vaccine (IDB)
vaccination process that occurs in intradermal route.
vaccination process that occurs in intranasal route
vaccination process that occurs in oral route.
vaccination process that occurs in the subcutaneous route
a role inheres in the vaccine component when it is added into vaccine's formulation, it tends to stabilizes an emulsion by increasing its kinetic stablity.
a role inheres in vaccine component when added into vaccine's formulation, it tends to inhibit the reaction between two or more other vaccine substances in the final vaccine formulation; it also helps to protect the vaccine from adverse conditions such as the freeze-drying process or heat.
The conjugate protein is a part of a conjugate vaccine and acts as a carrier protein that is covalently attached to a vaccine antigen with poor antigenicity (e.g., a polysaccharide). A conjugate protein is able to induce T-cell-dependent immune responses and stimulate the production of immune memory.
role inheres in a material eneitity that union itself chemically with a relative weak vaccine antigen to form a new whole that can create an effective miinuogen. The
epicutaneous (application onto the skin), e
Administration of a drug by the way of absorption through the skin, usually for systemic action. The route allows sustained therapeutic plasma drug levels and avoids first pass effect. Simplicity of administration tends to result in high patient compliance.
The injection of a given substance directly into the bladder via a urethral catheter instead of being injected under the skin.
BCG Vaccine (Freeze-Dried) (by Sanofi Pasteur)
Product Name: Hepatitis B Vaccine (Recombinant)
A Measles-Rubella vaccine that is live attenuated and manufactured by GlaxoSmithKline Biologicals.
Trade Name: Inactived Poliomyelitis Vaccine - IPV
todo: Proteins + killed viruses + conjugate
todo: Proteins + killed virus + conjugate
Trade Name: Meningococcal Polysaccharide Vaccine, Groups A & C, Menomune A/C
Meningococcal Polysaccharide Vaccine, Groups A & C, Menomune A/C
A live attenuated V. cholerae vaccine that is manufactured by Berna Biotech, Ltd. This vaccine uses the V. Cholera strain CVD 103-HGR.
todo: Proteins, killed virus + conjugate
A MMR vaccine that is manufactured by GlaxoSmithKline Biologicals.
A Measles-Mumps-Rubella-Vericella vaccine that is live attenuated and manufactured by GlaxoSmithKline Biologicals.
todo: Recombinant protein + killed virus
todo: assign parent immunogen: Typh-I + (HA)
A vaccine that protects against Haemophilus influenzae.
A vaccine that protects against Tick-borne Encephalitis Virus (TBEV).
Tick-borne Encephalitis Virus (TBEV) vaccine
administration process
number corresponding to a person's apartment
apartment number
a biological molecule involved in a metabloic pathway
biochemical entity
biological entity
the date which a person is born
birthdate
a process which occurs in the body
bodily process
number corresponding to a person's apartment building
building number
a major metropolitan center of a region
city
the location of a clinic or physician's ofice
clinic address
A Geopolitical Entity that delimits a Government with effective internal and external sovereignty over the region and its population, and which is not dependent on or subject to any other power or Geopolitical Entity.
country
digital address
the address a person can receive and send electronic messages
A reference to a place on the Earth, by its name or by its geographical location.
geographic location
the place where a person or organization is located or may be reached
home address
form of identification
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
immune response
identifiers
a combination of words by which a person is called
name
regional government within a country
state
a public roadway in a village, town, or city
street
the cellular number where a person can be reached
telephone
vaccine data item
a unique identifier assigned to a specific batch of a vaccine
vaccine lot number
the succession of vaccinations provided for a particular disease
vaccine series number
The date assigned by the manufacturer on which the vaccine should no longer be used
vaccine expiration date
a variant of the HPV vaccine which targets 9 HPV strains
Gardasil 9
HPV strain
HPV 11
HPV 16
HPV 18
HPV 31
HPV 33
HPV 45
HPV 52
HPV 58
HPV 6
vaccination against HepB infection
HepB vaccination
hispanic or latino
not hispanic or latino
American Indian or Alaska Native
Asian
Black or African American
Native Hawaiian or Other Pacific Islander
White
component related to HPV
HPV entity
the infectious units of papillomaviruses
papillomavirus particles
A physical entity consisting of a sequence of amino acids; a protein monomer; a single polypeptide chain.
protein
non-infectious, virus-derived structures that mimic the form and size of a virus but lack the genetic material necessary for replication
virus-like particles
protein which facilitates the early spead of papillomavirus
gene and protein which encodes for HPV strain
Immunoglobulin molecules having a specific amino acid sequence by virtue of which they interact only with the ANTIGEN (or a very similar shape) that induced their synthesis in cells of the lymphoid series
antibodies
An action specification comprising the number of doses and their timing for a vaccination of an individual organism against a specific infectious agent.
vaccination schedule
the age in which a person is eligible to receive a vaccine
age of eligibility
the minimum interval of time for successive doses of a vaccine to be administeres
min interval between
minimum age it is recommended for a vaccine to be administeres
min overdue age
minimum age required to receive the immunization
min rec age
the minimum reccomended interval for administration
min rec interval
interval of time where it is not recommended to administer successive doses
overdue interval between
laryngeal cancer
health care provider
doctor
vaccine administrator
A pubic safety employee or volunteer whose duties include responding rapidly to an emergency
first responder
gender identifier
date of birth
male gender identifier
female gender identifier
intersex gender identifier
transgender identifier
vaccination dose
hpv-related cancer
oropharyngeal cancer
penile cancer
vaginal cancer
cervical cancer
anal cancer
vulvar cancer
a place with a group of physicians dedicated to the treatment of patients
health care clinic
pharmaceutical company
viral infection
human papilllomavirus infection
upper deltoid
cervical changes
genital warts
skin itchiness
skin warts
the act of disclosing valuable information
disclosure
minor informed consent form
sheets that explain both the benefits and risks of a vaccine to vaccine recipients
Vaccine Information Statement
immunization registry
hpv vaccination informed consent process
hpv vaccination patient
hpv vaccine administrator
Gardasil vaccination dose
First Gardasil vaccination dose
Second Gardasil vaccination dose
Third Gardasil vaccination dose
Gardasil HPV vaccination
Gardasil 9 HPV vaccination
Cervarix HPV vaccination
Gardasil 9 vaccination dose
First Gardasil 9 vaccination dose
Second Gardasil 9 vaccination dose
Cervarix vaccination dose
First Cervarix vaccination dose
Second Cervarix vaccination dose
Third Cervarix vaccination dose
human papillomavirus vaccination
vaccination history
immunization record
allergic reaction history
a system used in the U.S. consisting of a five-digit code
zip code
1a: The part of the face that bears the nostrils and covers the anterior part of the nasal cavity; broadly: this part together with the nasal cavity.n1b: The anterior part of the head at the top or end of the muzzle: snout, proboscis.n2: The vertebrate olfactory organ.[accessedResource: BTO:0000840][accessDate: 05-04-2011]
Any sense organ (FBbt:00005155) that functions in (some) detection of chemical stimulus involved in sensory perception (GO:0050907).[accessedResource: FBbt:00005157][accessDate: 05-04-2011]
Nose[accessedResource: FMAID:46472][accessDate: 05-04-2011]
chemosensory sensory organ[accessedResource: FBbt:00005157][accessDate: 05-04-2011]
olfactory system[accessedResource: TAO:0001149][accessDate: 05-04-2011]
*Subdivision of face which consists of the nasal skeleton, nasal septum and nasal cavity.
1a: The part of the face that bears the nostrils and covers the anterior part of the nasal cavity; broadly: this part together with the nasal cavity.n1b: The anterior part of the head at the top or end of the muzzle: snout, proboscis.n2: The vertebrate olfactory organ.
1a: The part of the face that bears the nostrils and covers the anterior part of the nasal cavity; broadly: this part together with the nasal cavity.nb: The anterior part of the head at the top or end of the muzzle: snout, proboscis.n2. The vertebrate olfactory organ.
Any sense organ (FBbt:00005155) that functions in (some) detection of chemical stimulus involved in sensory perception (GO:0050907).
Any sense organ (FBbt:00005155) that has function 'detection of chemical stimulus involved in sensory perception (GO:0050907)'.
A state on the West Coast of the United States, along the Pacific Ocean. It is bordered by Oregon to the north, Nevada to the east, Arizona to the southeast, and to the south the Mexican state of Baja California.
A state in the Pacific Northwest region of the United States. Oregon is located on the Pacific coast between Washington to the north, California to the south, Nevada on the southeast and Idaho to the east. The Columbia and Snake rivers delineate much of Oregon's northern and eastern boundaries respectively.
A state located in the southwestern region of the United States. It borders New Mexico, Utah, Nevada, California, touches Colorado, and has a 626 km international border with the States of Sonora and Baja California in Mexico.
A state located in the Mid Atlantic region of the United States, bordering Virginia, West Virginia and the District of Columbia to the south and west, Pennsylvania to the north, and Delaware to the east.
A state located on the Atlantic Seaboard in the southeastern United States. The state borders South Carolina and Georgia to the south, Tennessee to the west and Virginia to the north.
A state in the United States of America, in the extreme northwest portion of the North American continent. The state is bordered by Yukon Territory and British Columbia, Canada to the east, the Gulf of Alaska and the Pacific Ocean to the south, the Bering Sea, Bering Strait, and Chukchi Sea to the west, and the Beaufort Sea and the Arctic Ocean.
A state in the southern region (Deep South) of the United States. It borders Georgia to the south and North Carolina to the north.
A state in the New England region of the United States. By land Rhode Island borders Connecticut to the west and Massachusetts to the north and east. Rhode Island also shares a water border with New York to the southwest.
State of Rhode Island and Providence Plantations
A state in the northwestern region of the United States. Wyoming is bordered on the north by Montana, on the east by South Dakota and Nebraska, on the south by Colorado, on the southwest by Utah, and on the west by Idaho.
A state located in the New England region of the northeastern United States. It borders Rhode Island and Connecticut to the south, New York to the west, and Vermont and New Hampshire to the north. To the east, it borders the Atlantic Ocean.
A state in the Midwestern region of the United States. The state shares a Lake Superior water border with Michigan and Wisconsin on the northeast; the remainder of the eastern border is with Wisconsin. Iowa is to the south, North Dakota and South Dakota to the west, and the Canadian provinces of Ontario and Manitoba to the north.
A state located in the Northeastern and Middle Atlantic regions of the United States. The state borders Delaware and Maryland to the south, West Virginia to the southwest, Ohio to the west, New York and Canada to the north, and New Jersey to the east.
A state located in the South Central region and Southern Region of the United States of America. It is bounded on the east by Arkansas and Missouri, on the north by Kansas, on the northwest by Colorado, on the far west by New Mexico, and on the south and near-west by Texas.
The Northwestern-most state of the contiguous United States. Its northern border lies mostly along the 49th parallel, and then via marine boundaries through the Strait of Georgia, Haro Strait and Strait of Juan de Fuca, with the Canadian province of British Columbia to the north. Washington borders Oregon to the south, with the Columbia River forming most of the boundary and the 46th parallel forming the eastern part of the southern boundary. To the east Washington borders Idaho, bounded mostly by the meridian running north from the confluence of the Snake River and Clearwater River, except for the southernmost section where the border follows the Snake River. To the west of Washington lies the Pacific Ocean.
A state in the Mid-Atlantic and Northeastern regions of the United States. It is bordered on the north by New York, on the east by the Atlantic Ocean, on the southwest by Delaware, and on the west by Pennsylvania. New Jersey lies within the sprawling metropolitan areas of New York and Philadelphia.
A state located in the South Central United States. The Rio Grande, Red River and Sabine River form natural state borders, Oklahoma on the north, Louisiana and Arkansas on the east, and the Mexican states of Chihuahua, Coahuila, Nuevo Leon, and Tamaulipas to the south.
A State located in the north-central part of the United States. Wisconsin is bordered by the Montreal River; Lake Superior and Michigan to the north; by Lake Michigan to the east; by Illinois to the south; and by Iowa and Minnesota to the west. The state's boundaries include the Mississippi River and Saint Croix River in the west, and the Menominee River in the northeast Wisconsin's capital is Madison, and its largest city is Milwaukee.
A state located in the New England region of the northeastern United States of America. The state borders New York to the west and south (Long Island by sea), Massachusetts to the north, and Rhode Island to the east. Portions of southwestern Connecticut are considered part of the New York metropolitan area.
A state in the New England region of the northeastern United States of America, bordering the Atlantic Ocean to the southeast, New Hampshire to the southwest, the Canadian provinces of Quebec to the northwest and New Brunswick to the northeast.
A state in the Western United States. To the north, Montana and Canada share a 877 km border. The state borders the Canadian provinces of British Columbia, Alberta, and Saskatchewan. To the east, the state borders North Dakota and South Dakota. To the south is Wyoming and to the west and southwest is Idaho.
Georgia is bordered on the south by Florida; on the east by the Atlantic Ocean and South Carolina; on the west by Alabama and by Florida in the extreme southwest; and on the north by Tennessee and North Carolina. The northern part of the state is in the Blue Ridge Mountains, a mountain range in the vast mountain system of the Appalachians. The central piedmont extends from the foothills to the fall line, where the rivers cascade down in elevation to the continental coastal plain of the southern part of the state.
A state located on the Atlantic Coast in the Mid-Atlantic region of the United States. Delaware is located in the eastern section of the Delmarva Peninsula, between Delaware Bay and Chesapeake Bay. Delaware is bounded to the north by Pennsylvania; to the east by the Delaware River, Delaware Bay, New Jersey and the Atlantic Ocean; and to the west and south by Maryland.
A state located in the southeastern region of the United States, bordering Alabama to the northwest and Georgia to the northeast. Much of the land mass of the state is a large peninsula with the Gulf of Mexico to the west and south, and the Atlantic Ocean to the east.
A midwestern state of the United States of America. The Northeastern border of Illinois is Lake Michigan. Its eastern border with Indiana is all of the land west of the Wabash River, and a north-south line above Post Vincennes, or 87deg31min30secW. Its northern border with Wisconsin is fixed at 42deg30minN. Its western border with Missouri and Iowa is the Mississippi River. Its southern border with Kentucky is the Ohio River. Illinois also borders Michigan, but only via a water boundary in Lake Michigan.
A Midwestern state of the United States of America. Michigan consists of two peninsulas that lie between 82deg30minW to about 90deg30minW longitude, and are separated by the Straits of Mackinac. With the exception of two small areas that are drained by the Mississippi River by way of the Wisconsin River in the Upper Peninsula and by way of the Kankakee-Illinois River in the Lower Peninsula, Michigan is drained by the Great Lakes-Saint Lawrence watershed. The Great Lakes that border Michigan from east to west are Lake Erie, Lake Huron, Lake Michigan and Lake Superior. The state is bounded on the south by the states of Ohio and Indiana, sharing land and water boundaries with both.
A state on the Atlantic Coast of the Southern United States. Virginia is bordered by Maryland and the District of Columbia to the north and east; the Atlantic Ocean to the east; by North Carolina and Tennessee to the south; by Kentucky to the west and by West Virginia to the north and west. Due to a peculiarity of Virginia's original charter, its boundary with Maryland does not extend past the low-water mark of the southern shore of the Potomac River, so Maryland and the District of Columbia contain the whole width of the river rather than splitting it between them and Virginia. The southern border is defined as the 36deg30min parallel north.
A state in the United States, located on an archipelago in the central Pacific Ocean southwest of the continental United States, southeast of Japan, and northeast of Australia.
A state located in the Southern United States. The capital city is Nashville, and the largest city is Memphis. Tennessee borders eight other states: Kentucky and Virginia to the north; North Carolina to the east; Georgia, Alabama and Mississippi on the south; Arkansas and Missouri on the Mississippi River to the west.
A western state of the United States. Utah has three distinct geological regions: the Rocky Mountains, the Great Basin, and the Colorado Plateau.
A state in the Appalachian, Upland South, and Mid-Atlantic regions of the United States, bordered by Virginia on the southeast, Kentucky on the southwest, Ohio on the northwest, and Pennsylvania and Maryland on the northeast. The capital and largest city is Charleston.
A Midwestern state of the United States. Ohio's southern border is defined by the Ohio River (with the border being at the 1793 low-water mark on the north side of the river), and much of the northern border is defined by Lake Erie. Ohio's neighbors are Pennsylvania to the east, Michigan to the northwest, Ontario Canada, to the north, Indiana to the west, Kentucky on the south, and West Virginia on the southeast.
A state located in the southwestern region of the United States.
A state in the New England region of the northeastern United States of America. It borders Massachusetts to the south, Vermont to the west, Maine to the east, and the Canadian province of Quebec to the north.
A state in the New England region of the northeastern United States of America. It is bordered by Massachusetts to the south, New Hampshire to the east, New York to the west, and the Canadian province of Quebec to the north.
A state located in the Deep South of the United States. Jackson is the state capital and largest city. Mississippi is bordered on the north by Tennessee, on the east by Alabama, on the south by Louisiana and a narrow coast on the Gulf of Mexico, and on the west, across the Mississippi River, by Louisiana and Arkansas.
A state in the Midwest region of the United States. Missouri is bounded on the north by Iowa; on the east, across the Mississippi River, by Illinois, Kentucky, and Tennessee; on the south by Arkansas; and on the west by Oklahoma, Kansas, and Nebraska (the last across the Missouri River).
A state located in the southern region of the United States of America. Louisiana is bordered to the west by the State of Texas; to the north by Arkansas; to the east by the State of Mississippi; and to the south by the Gulf of Mexico.
A state in the central region of the United States of America. Kansas is bordered by Nebraska on the north; Missouri on the east; Oklahoma on the south; and Colorado on the west.
A state located in the Midwestern region of the United States of America. Iowa is bordered by the Mississippi River on the east; the Missouri River and the Big Sioux River on the west; the northern boundary is a line along 43 degrees, 30 minutes north latitude. The southern border is the Des Moines River and a line along approximately 40 degrees 35 minutes north.
A midwestern state of the United States of America. Indiana is bounded on the north by Lake Michigan and the state of Michigan; on the east by Ohio; on the south by Kentucky, with which it shares the Ohio River as a border; and on the west by Illinois. Indiana is one of the Great Lakes states.
A state located in the East Central United States of America. Kentucky borders on seven states, from both the Midwest and the Southeast. West Virginia lies to the east, Virginia to the southeast, Tennessee to the south, Missouri to the west, Illinois and Indiana to the northwest, and Ohio to the north and northeast.
A state located in the southern region of the United States. Arkansas shares a border with six states, with its eastern border largely defined by the Mississippi River. Arkansas shares its southern border with Louisiana, its northern border with Missouri, its eastern border with Tennessee and Mississippi, and its western border with Texas and Oklahoma.
A state located in the Midwestern and Western regions of the United States of America.
A state located in the Midwestern region of the United States of America.
A state located in the western region of the United States of America. Nevada is almost entirely within the Basin and Range Province, and is broken up by many north-south mountain ranges. Most of these ranges have endorheic valleys between them, which belies the image portrayed by the term Great Basin. The southern third of the state, where the Las Vegas area is situated, is within the Mojave Desert.
A state located on the Great Plains of the Midwestern United States and Western United States.
A state located in the Rocky Mountain region of the United States of America.
A state in the Pacific Northwest region of the United States of America. Idaho borders six states and one Canadian province, but does not border the Pacific Ocean at any point and is not, as such, a coastal state. The states of Washington and Oregon are to the west, Nevada and Utah are to the south, and Montana and Wyoming are to the east. The province of British Columbia, to the north, also shares a small (77 km) border with Idaho.
A state located in the southern region of the United States of America. It is bordered by Tennessee to the north, Georgia to the east, Florida and the Gulf of Mexico to the south, and Mississippi to the west.
A public research university located in the city of College Park in Prince George's County, Maryland.
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.
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.
The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality.
This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore).
Аҧсуа бызшәа
Аҧсшәа
Abkhazian
Achinese
Acoli
Adangme
Adygei
Adyghe
Afrihili
Afrikaans
Ainu
Akan
Akkadian
Shqip
Albanian
Aleut
Southern Altai
አማርኛ
Amharic
English, Old (ca.450–1100)
Angika
العَرَبِيَّة
Arabic
Imperial Aramaic (700–300 BCE)
Official Aramaic (700–300 BCE)
aragonés
Aragonese
Հայերեն
Հայերէն
Armenian
Mapuche
Mapudungun
Arapaho
Arawak
অসমীয়া
Assamese
Asturleonese
Bable
Leonese
Asturian
Авар мацӏ
Магӏарул мацӏ
Avaric
Avestan
Awadhi
Aymar aru
Aymara
Azərbaycan dili
Азәрбајҹан дили
آذربایجان دیلی
Azerbaijani
Başqort tele
Башҡорт теле
Bashkir
Baluchi
ߓߊߡߊߣߊߣߞߊߣ
Bambara
Balinese
euskara
Basque
Basa
Bedawiyet
Beja
Беларуская мова
Belarusian
Bemba
বাংলা
Bengali
Bhojpuri
Bikol
Edo
Bini
Bislama
Siksika
བོད་སྐད་
ལྷ་སའི་སྐད་
Tibetan
bosanski
босански
Bosnian
Braj
Brezhoneg
Breton
Buriat
Buginese
български език
Bulgarian
မြန်မာစကား
မြန်မာစာ
Burmese
Bilin
Blin
Caddo
Galibi Carib
Valencian
català
Catalan
Cebuano
český jazyk
čeština
Czech
Finu' Chamoru
Chamorro
Chibcha
Нохчийн мотт
نَاخچیین موٓتت
ნახჩიე მუოთთ
Chechen
Chagatai
中文
汉语
漢語
Chinese
Chuukese
Mari
Chinook jargon
Choctaw
Dene Suline
Chipewyan
Cherokee
Church Slavonic
Old Bulgarian
Old Church Slavonic
Old Slavonic
Славе́нскїй ѧ҆зы́къ
Church Slavic
Чӑвашла
Chuvash
Cheyenne
Montenegrin
Coptic
Kernowek
Cornish
Corsu
Lingua corsa
Corsican
Cree
Crimean Turkish
Crimean Tatar
Kashubian
Cymraeg
y Gymraeg
Welsh
Dakota
dansk
Danish
Dargwa
Delaware
Slave (Athapascan)
Deutsch
German
Dogrib
Dinka
Dhivehi
Maldivian
ދިވެހި
ދިވެހިބަސް
Divehi
Dogri
Lower Sorbian
Duala
Dutch, Middle (ca. 1050–1350)
Flemish
Nederlands
Vlaams
Dutch
Dyula
རྫོང་ཁ་
Dzongkha
Efik
Egyptian (Ancient)
Ekajuk
Νέα Ελληνικά
Greek, Modern (1453–)
Elamite
English
English, Middle (1100–1500)
Esperanto
eesti keel
Estonian
Èʋegbe
Ewe
Ewondo
Fang
føroyskt
Faroese
فارسی
Persian
Fanti
Na Vosa Vakaviti
Fijian
Pilipino
Filipino
suomen kieli
Finnish
Fon
français
French
French, Middle (ca. 1400–1600)
French, Old (842–ca. 1400)
Northern Frisian
Eastern Frisian
Frysk
Western Frisian
Fulfulde
Pulaar
Pular
Fulah
Friulian
Gayo
Gbaya
ქართული
Georgian
Geez
Gilbertese
Gàidhlig
Scottish Gaelic
Gaelic
Gaeilge
Irish
galego
Galician
Gaelg
Gailck
Manx
German, Middle High (ca. 1050–1500)
German, Old High (ca. 750–1050)
Gondi
Gorontalo
Gothic
Grebo
Greek, Ancient (to 1453)
Avañe'ẽ
Guarani
Alemannic
Alsatian
Swiss German
ગુજરાતી
Gujarati
Gwich'in
Haida
Haitian Creole
kreyòl ayisyen
Haitian
Harshen Hausa
هَرْشَن
Hausa
Hawaiian
עברית
Hebrew
Otjiherero
Herero
Hiligaynon
हिन्दी
Hindi
Hittite
Mong
Hmong
Hiri Motu
hrvatski
Croatian
Upper Sorbian
magyar nyelv
Hungarian
Hupa
Iban
Asụsụ Igbo
Igbo
íslenska
Icelandic
Ido
Nuosu
ꆈꌠꉙ
Sichuan Yi
ᐃᓄᒃᑎᑐᑦ
Inuktitut
Occidental
Interlingue
Iloko
Interlingua ( International Auxiliary Language Association )
bahasa Indonesia
Indonesian
Ingush
Iñupiaq
Inupiaq
italiano
lingua italiana
Italian
ꦧꦱꦗꦮ
Javanese
Lojban
日本語
Japanese
Judeo-Persian
Judeo-Arabic
Kara-Kalpak
Kabyle
Jingpho
Kachin
Greenlandic
Kalaallisut
Kamba
ಕನ್ನಡ
Kannada
كأشُر
कॉशुर
Kashmiri
Kanuri
Kawi
qazaq tili
қазақ тілі
Kazakh
Kabardian
Khasi
ភាសាខ្មែរ
Central Khmer
Sakan
Khotanese
Gikuyu
Gĩkũyũ
Kikuyu
Kinyarwanda
Kyrgyz
кыргыз тили
кыргызча
Kirghiz
Kimbundu
Konkani
Коми кыв
Komi
Kongo
한국어
Korean
Kosraean
Kpelle
Karachay-Balkar
Karelian
Kurukh
Kwanyama
Kuanyama
Kumyk
Kurdî
کوردی
Kurdish
Kutenai
Ladino
Lahnda
Lamba
ພາສາລາວ
Lao
Lingua latīna
Latin
Latviešu valoda
Latvian
Lezghian
Limburger
Limburgish
Lèmburgs
Limburgan
Lingala
lietuvių kalba
Lithuanian
Mongo
Lozi
Letzeburgesch
Lëtzebuergesch
Luxembourgish
Luba-Lulua
Kiluba
Luba-Katanga
Luganda
Ganda
Luiseno
Lunda
Luo (Kenya and Tanzania)
Lushai
македонски јазик
Macedonian
Madurese
Magahi
Kajin M̧ajeļ
Marshallese
Maithili
Makasar
മലയാളം
Malayalam
Mandingo
Te Reo Māori
Maori
मराठी
Marathi
Masai
Bahasa Melayu
Malay
Moksha
Mandar
Mende
Irish, Middle (900–1200)
Micmac
Mi'kmaq
Minangkabau
Malagasy
Malti
Maltese
Manchu
Manipuri
Mohawk
монгол хэл
ᠮᠣᠩᠭᠣᠯ ᠬᠡᠯᠡ
Mongolian
Mossi
Creek
Mirandese
Marwari
Erzya
Neapolitan
dorerin Naoero
Nauru
Diné bizaad
Naabeehó bizaad
Navaho
Navajo
South Ndebele
isiNdebele seSewula
Ndebele, South
North Ndebele
siNdebele saseNyakatho
Ndebele, North
ndonga
Ndonga
German, Low
Low Saxon
Saxon, Low
Low German
नेपाली भाषा
Nepali
Newari
Nepal Bhasa
Nias
Niuean
Nynorsk, Norwegian
nynorsk
Norwegian Nynorsk
Norwegian Bokmål
bokmål
Bokmål , Norwegian
Nogai
Norse, Old
norsk
Norwegian
N'Ko
Northern Sotho
Sepedi
Pedi
Classical Nepal Bhasa
Old Newari
Classical Newari
Chewa
Chichewa
Chinyanja
Nyanja
Nyamwezi
Nyankole
Nyoro
Nzima
Provençal
lenga d'òc
occitan
provençal
Occitan (post 1500)
Ojibwa
ଓଡ଼ିଆ
Oriya
Afaan Oromoo
Oromo
Osage
Ossetic
Ирон æвзаг
Ossetian
Turkish, Ottoman (1500–1928)
Pangasinan
Pahlavi
Kapampangan
Pampanga
Punjabi
پنجابی
ਪੰਜਾਬੀ
Panjabi
Papiamento
Palauan
Persian, Old (ca. 600–400 B.C.)
Phoenician
Pāli
Pali
Język polski
Polish
Pohnpeian
português
Portuguese
Old Occitan (to 1500)
Provençal, Old (to 1500)
Pashto
پښتو
Pushto
Nuna shimi
Runa simi
kichwa simi
Quechua
Rajasthani
Rapanui
Cook Islands Maori
Rarotongan
Romauntsch
Romontsch
Rumantsch
Rumàntsch
Romansh
Romany
Moldavian
Moldovan
limba română
Romanian
Ikirundi
Rundi
Arumanian
Macedo-Romanian
Aromanian
русский язык
Russian
Sandawe
yângâ tî sängö
Sango
Yakut
Samaritan Aramaic
संस्कृतम्
Sanskrit
Sasak
Santali
Sicilian
Scots
Selkup
Irish, Old (to 900)
Shan
Sidamo
Sinhalese
සිංහල
Sinhala
slovenský jazyk
slovenčina
Slovak
slovenski jezik
slovenščina
Slovenian
Southern Sami
davvisámegiella
Northern Sami
Lule Sami
Inari Sami
Gagana faʻa Sāmoa
Samoan
Skolt Sami
chiShona
Shona
سنڌي
सिन्धी
ਸਿੰਧੀ
Sindhi
Soninke
Sogdian
af Soomaali
Somali
Sesotho [southern]
Sotho, Southern
Castilian
castellano
español
Spanish
limba sarda
lingua sarda
sardu
Sardinian
Sranan Tongo
srpski
српски
Serbian
Serer
siSwati
Swati
Sukuma
Basa Sunda
ᮘᮞ ᮞᮥᮔ᮪ᮓ
Sundanese
Susu
Sumerian
Kiswahili
Swahili
svenska
Swedish
Classical Syriac
Syriac
Reo Mā'ohi
Reo Tahiti
Tahitian
தமிழ்
Tamil
tatar tele
татар теле
تاتار
Tatar
తెలుగు
Telugu
Timne
Tereno
Tetum
tojikī
тоҷикӣ
Tajik
Wikang Tagalog
Tagalog
ภาษาไทย
Thai
Tigre
ትግርኛ
Tigrinya
Tiv
Tokelau
tlhIngan-Hol
Klingon
Tlingit
Tamashek
Tonga (Nyasa)
lea faka-Tonga
Tonga (Tonga Islands)
Tok Pisin
Tsimshian
Setswana
Tswana
Xitsonga
Tsonga
Türkmençe
türkmen dili
Түркменче
түркмен дили
تورکمن تیلی
تورکمنچه
Turkmen
Tumbuka
Türkçe
Turkish
Tuvalu
Twi
Tuvinian
Udmurt
Ugaritic
Uyghur
ئۇيغۇر تىلى
ئۇيغۇرچە
Uighur
українська мова
Ukrainian
Umbundu
اُردُو
Urdu
Oʻzbekcha
oʻzbek tili
ўзбек тили
ўзбекча
ئوبېک تیلی
ئوزبېچه
Uzbek
Vai
Tshivenḓa
Venda
Tiếng Việt
Vietnamese
Volapük
Votic
Walamo
Wolaytta
Wolaitta
Waray
Washo
Walon
Walloon
Wolof
Oirat
Kalmyk
isiXhosa
Xhosa
Yao
Yapese
אידיש
ייִדיש
יידיש
Yiddish
èdè Yorùbá
Yoruba
Zapotec
Bliss
Blissymbolics
Blissymbols
Zenaga
Standard Moroccan Tamazight
Chuang
Vahcuengh
話僮
Zhuang
isiZulu
Zulu
Zuni
Dimili
Dimli
Kirdki
Kirmanjki
Zazaki
Zaza
axiom holds for all times
Minatoba government Public Health division
Rite Aid
Costco
Walgreens
Have you had a disorder in the last month that caused brain or nerve damage such as stroke or convulsion?
GlaxoSmithKline Biologicals
Massachusetts Public Health Biologic Lab
Research Foundation for Microbial Diseases of Osaka University
Vaccine Adverse Event Reporting System (VAERS)
National Vaccine Injury Compensation Program (VICP)
ImmTrac2
A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into "census areas"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a "charter township", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county.
An unincorporated territory of the United States.
An area of the United States of America under United States jurisdiction, to which Congress has determined that only select parts of the United States of America Constitution apply.
An unincorporated territory of the United States located in the South Pacific Ocean, southeast of the sovereign State of Samoa. The main (largest and most populous) island is Tutuila, with the Manu'a Islands, Rose Atoll, and Swains Island also included in the territory.
A group of islands in the Caribbean that are an insular area of the United States. The islands are geographically part of the Virgin Islands archipelago and are located in the Leeward Islands of the Lesser Antilles. The US Virgin Islands are an organized, unincorporated United States territory. The US Virgin Islands are administratively divided into two districts and subdivided into 20 sub-districts.
A Micronesian island nation in the western Pacific Ocean, located north of Nauru and Kiribati, east of the Federated States of Micronesia and south of the United States territory of Wake Island, to which it lays claim.
A semi-autonomous territory composed of an archipelago in the northeastern Caribbean, east of the Dominican Republic and west of the Virgin Islands, approximately 2,000 km off the coast of Florida (the nearest of the mainland United States).
A commonwealth in political union with the United States.
Commonwealth of the Northern Mariana Islands
An unorganized, unincorporated territory of the United States, administered by the Office of Insular Affairs, US Department of the Interior.
A statistical designation defined by ISO3166-1, consists of nine insular United States possessions. Palmyra Atoll is the only incorporated territory of the United States. Currently, none of the islands have any permanent residents.
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.
has_specified_output
The inverse property of is specified output of
The inverse property of is_specified_output_of
has specified output
non-binary gender identity datum
A gender identity datum resulting from a gender identification process in which ‘non binary’ is selected based on the participant's subjective sense of gender.
Paul Fabry
Afaraf
Qafar af
Qafaraf
’Afar Af
non-binary gender identity information content entity
Alternatively: A gender identity datum stating that a person's subjective sense of gender is non-binary.) Examples of usage: ‘Non-binary’, ‘Trigender’, ‘Agender’, ‘Genderfluid’, ‘2’ (intended to refer to a non-binary gender role)
Afar
obsolete non-binary gender identity datum
A material entity consisting of multiple components that are causally integrated.
May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
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).