Barry Smith
Chris Stoeckert
Daniel Welch
Jie Zheng
John W. Judkins
Matthew Diller
S. Clint Dowland
Sam Smith
Sarah Bost
Selja Seppälä
William D. Duncan
Yongqun He
Amanda Hicks
Mathias Brochhausen
Shariq Tariq
Swetha Garimalla
William Hogan
The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations.
Ontology for Modeling and Representation of Social Entities
This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's "meaningful use" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
BFO CLIF specification label
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
editor preferred label
example of usage
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
definition editor
alternative label
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.
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).
alternative term
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
has_MedDRA_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.
The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing).
A provenance property that denotes a synonym to be the preferred one for a specific community.
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.
OOSTT user-centered description
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
temporal interpretation
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
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/
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
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])
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])
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
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
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
is about
An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
PERSON: Jonathan Rees
Person: Alan Ruttenberg
mentions
Inverse of the relation 'mentions'
mentioned by
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q
8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
is quality measurement of
inverse of the relation 'denotes'
Person: Jie Zheng, Chris Stoeckert, Mike Conlon
denoted by
relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
has coordinate unit label
relates a process to a time-measurement-datum that represents the duration of the process
is duration of
inverse of the relation of is quality measurement of
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
is quality measured as
A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality.
Person:Bjoern Peters
is quality specification of
inverse of the relation of is quality specification of
quality is specified as
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
has time stamp
relates a time stamped measurement datum to the measurement datum that was measured
has measurement datum
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
has_specified_input
see is_input_of example_of_usage
The inverse property of is_specified_input_of
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Alan Ruttenberg
is_specified_input_of
has_specified_output
The inverse property of is specified output of
The inverse property of is_specified_output_of
has specified output
is_specified_output_of
A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
A 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
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
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.
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 is a characteristic of this vase
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.
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 bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
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.
has_participant
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
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.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
disposition of
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
location_of
location of
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
located_in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
the surface of my skin is a 2D boundary of my body
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
2D_boundary_of
boundary of
is 2D boundary of
is boundary of
2D boundary of
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
has boundary
has_2D_boundary
has 2D boundary
A 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
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
p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
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 provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.
provides input for
transitive form of directly_provides_input_for
This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'.
transitively provides input for
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.
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
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.
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
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
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
independent continuant
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
two-dimensional spatial region
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal region
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
zero-dimensional spatial region
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (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]
specifically dependent continuant
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object part
an edge of a cube-shaped portion of space.
A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
one-dimensional spatial region
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
object
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
the boundary between the 2nd and 3rd year of your life.
p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
the temporal region during which a process occurs.
BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
Every continuant fiat boundary is located at some spatial region at every time at which it exists
(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
continuant fiat boundary
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
one-dimensional continuant fiat boundary
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
a marriage bond, an instance of requited love, an obligation between one person and another.
b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
relational quality
a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
two-dimensional continuant fiat boundary
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
zero-dimensional continuant fiat boundary
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii). Note: this definition was taken over from "geopolitical organization".
IMPORTANT: The label "geopolitical organization" was previously used for OMRSE_00000044 (governmental organization). "geopoli organization" is a label for a new and different class.
governmental organization
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: Melanie Courtot
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
narrative object
Examples of narrative objects are reports, journal articles, and patents submission.
A narrative object is an information content entity that is a set of propositions.
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
person:Chris Stoeckert
Pour the contents of flask 1 into flask 2
A directive information entity that describes an action the bearer will take.
OBI Plan and Planned Process branch
action specification
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.
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://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
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
directive information entity
time trigger
obsolete_study interpretation
A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses
2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application."
2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead.
Lawrence Hunter
dot plot
Dot plot of SSC-H and FSC-H.
A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
person:Allyson Lister
graph
A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
PERSON: Lawrence Hunter
text based digital entity
XML file, C++ source code file
A text based digital entity is a digital entity that is encoded so that it only contains text characters.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document'
obsolete2_text based digital entity
rule
example to be added
A rule is an executable which guides, defines, restricts actions.
MSI
PRS
contour plot
Contour plot of SSC-H, FSC-H, and FL1-H.
generically_dependent_continuants
group:Flow Cytometry community
report figure
A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report
Replaced by defined version of figure
obsolete2_report figure
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
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, 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
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
A planned process in which a document is created or added to by including the specified input in it.
6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
Bjoern Peters
wikipedia http://en.wikipedia.org/wiki/Documenting
documenting
line graph
A line graph is a type of graph created by connecting a series of data points together with a line.
line chart
WEB: http://en.wikipedia.org/wiki/Line_chart
A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
Person:Melanie Courtot
assigning a centrally registered identifier
Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them.
A planned process in which a CRID registry associates an information content entity with a CRID symbol
associating information with a CRID in the CRID registry
associating information with a centrally registered identifier in its registry
a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Bill Hogan
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
centrally registered identifier
PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles.
A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process.
Justin Whorton
centrally registered identifier registry
Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID.
A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
looking up a centrally registered identifier
time stamped measurement datum
pmid:20604925 - time-lapse live cell microscopy
A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
experimental time series
time sampled measurement data set
written name
"Bill Clinton"
"The Eiffel Tower"
"United States of America"
A textual entity that denotes a particular in reality.
The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.
A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
PERSON: Michel Dumontier
software method
A software module is software composed of a collection of software methods.
PERSON: Melanei Courtot
software module
A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
software library
A software application is software that can be directly executed by some processing unit.
software application
A software script is software whose instructions can be executed using a software interpreter.
software script
abbreviation textual entity
From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect.
A textual entity listing abbreviations and their expansions that are used in a document.
PERSON: Bill Baumgartner
abbreviations section
The section labelled 'abbreviations' in a typical scientific journal article.
A part of a document where abbreviations and their long-forms used within the document are listed.
abbreviation and acronyms
abbreviation list
abbreviations
abbreviations and acronyms
abbreviations list
abbreviations used
definitions for abbreviations
list of abbreviations
list of abbreviations used
non-standard abbreviations
nonstandard abbreviations
nonstandard abbreviations and acronyms
author information section
The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/)
A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
author information
authors’ information
biographies
contributor information
author information textual entity
From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD.
A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
author summary section
The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/)
A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers.
author summary
summary
synopsis
Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)
author summary textual entity
From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX.
A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).
availability section
The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained.
availability
availability of data
data archiving
data availability
data availability statement
data sharing statement
availability textual entity
From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): Project home page:http://krux.googlecode.com
A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained.
case report section
The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/)
A part of a document about the medical history of a specific patient as it relates to the topic of the document.
case presentation
case report
case report textual entity
Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension.
A textual entity that expresses a detailed account of a portion of the medical history for a specific patient.
conclusion section
The section labelled 'conclusion' in a typical scientific journal article.
A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document.
concluding remarks
conclusion
conclusions
findings
conflict of interest section
The section labelled 'conflict of interest statement' in a typical scientific journal article.
A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document.
authors' disclosures of potential conflicts of interest
competing financial interests
competing interests
conflict of interest
conflict of interest statement
conflict of interests
conflicts of interest
declaration of competing interest
declaration of competing interests
declaration of interest
declaration of interests
disclosure of conflict of interest
disclosure of potential conflicts of interest
duality of interest
statement of interest
SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)]
A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document.
conflict of interest textual entity
consent section
The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)
A part of a document about the consent process that was used to enroll patients in a study.
consent
consent textual entity
From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal.
A textual entity that documents the consenting process used to enroll patients in a study.
ethical approval section
The section labelled 'ethical approval' in a typical scientific journal article.
A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis.
ethical approval
ethical requirements
ethics
ethics statement
ethical approval textual entity
From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review.
A textual entity that documents the ethical approval of some study design.
figures section
The section labelled 'figures' in a typical scientific journal article.
A part of a document that contains one or more figures.
figures
funding source declaration section
The section labelled 'funding' in a typical scientific journal article.
A part of a document used to detail information regarding the source of funding used in support of the generation of the document content.
financial support
funding
funding information
funding sources
funding statement
funding/support
grants
role of the funding source
source of funding
sources of funding
study funding
funding souce declaration textual entity
From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication.
A textual entity documenting the source of funding that supported some study.
funding source declaration textual entity
future directions section
The section labelled 'future directions' in a typical scientific journal article.
A part of a document detailing extensions of the described work that may be implemented at some future point in time.
future challenges
future considerations
future developments
future directions
future outlook
future perspectives
future plans
future prospects
future research
future research directions
future studies
future work
outlook
future directions textual entity
Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members.
A textual entity expressing ideas regarding future work relevant to work described in a document that could be done.
genome announcement section
The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/)
A document part announcing the publication of a novel draft genome sequence.
genome announcement
genome announcement textual entity
Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB).
A textual entity that describes the generation and public release of a novel, draft genome sequence.
keyword textual entity
From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): Exon orthology; alternative splicing; exon duplication; intron-exon structure.
A textual entity listing keywords indicating the major theme(s) of a document.
keywords section
The section labelled 'keywords' in a typical scientific journal article.
A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed.
keywords
study limitations section
The section labelled 'limitations' in a typical scientific journal article.
A part of a document about biases or short comings related to the study design and execution.
limitations
study limitations
Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
study limitations textual entity
Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out.
A textual entity addressing a shortcoming or bias of a study design or execution.
materials section
The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)
A part of a document about the materials required to reproduce the content of the document.
materials
notes section
The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):
A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc.
notes
patients section
The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/)
A part of a document about the patients that participated in a study.
patients textual entity
Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred.
A textual entity expressing information regarding the patients used in a study.
pre-publication history section
The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/)
A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors.
notice of republication
pre-publication history
pre-publication history textual entity
From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): The pre-publication history for this paper can be accessed here: http://www.biomedcentral.com/1471-2253/13/33/prepub
A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information.
related work section
The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/)
A part of a document about work in other publications that is relevant to the content of the document.
related literature
related work
related work textual entity
Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).
A textual entity that discusses work from other publications and expresses their relevancy to the content of a document.
requirements section
A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource.
requirements
requirements textual entity
From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): • Operating systems: Platform independent • Programming language: Matlab, R, Python • Other requirements: None • License: GNU GPL v3 • Any restrictions to use by non-academics: None
A textual entity that expresses the requirements necessary to use a resource, e.g. software.
statistical analysis textual entity
From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant.
A textual entity documenting statistical analysis tools and techniques employed.
statistical analysis section
The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)
A part of the document used to describe the statistical methodologies employed in the work presented in the document.
statistical analysis
tables section
The section labelled 'tables' in a typical scientific journal article.
A part of a document that contains one or more tables.
tables
An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail.
postal code
A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region.
Postal delivery route
A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes.
ZIP code
zone improvement plan code
database extract, transform, and load process
A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second.
Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second
Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output.
ETL
descriptive data section
A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made.
additional results section
A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.)
research participants section
A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.).
measurement methods section
A methods section that describes details of data assessment methods (data measurement).
research settings section
A document part that describes the physical/social/cultural conditions around a research trial.
study bias section
A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others.
graphical abstract
An abstract that is pictorial summary of the main findings described in the document.
visual abstract
A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistantly identify oneself as a human researcher or contributor.
"You can connect your iD with your professional information — affiliations, grants, publications, peer review, and more. You can use your iD to share your information with other systems, ensuring you get recognition for all your contributions, saving you time and hassle, and reducing the risk of errors." [https://orcid.org/]
This class was originally defined in Apollo_SV (http://purl.obolibrary.org/obo/APOLLO_SV_00000496) but due to it being more in scope of IAO, it was decided to add it to IAO and deprecate its Apollo_SV equivalent. (2022-10-25)
Open Researcher and Contributor Identifier
ORCID identifier
identifier
An 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 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.
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
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 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.
'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)
investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
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.
a planned process that carries out a study design
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 completely executed planned process that produces output data from input data.
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 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.
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
A document issued by a third party recognized as bearing the relevant authority to do so, that is designed to be about an entity's competence, qualifications, or authority.
A credential that is designed to be about an organism's competence or qualifications with respect to an occupation.
An organization that bears a credential grantor role.
An organism that an occupation credential is about.
A credential awarded by a credential granting agency designed to signify participation in or completion of a training program requiring the demonstration of some specified knowledge or skill.
A credential awarded by a professional organization designed to signify the holder's competence as measured against a specified professional benchmark.
A credential awarded by a government or government-authorized agency designed to signify legal authority to engage in specified actions without being liable to sanctions or penalties that would otherwise be associated with those actions.
A role borne by an organization that has been accredited by a quality assurance group through a deontic declaration having action regulation output, which authorizes the organization to bestow credentials according to quality control standards established or enforced by the accrediting group.
A social act in which a credential granting agency asserts that an organism has satisfied the requirements for being awarded a credential, having as output a credential about the organism.
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
healthcare 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.
healthcare role
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.
healthcare provider role
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.
healthcare provider organization role
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
organization healthcare role
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
obsolete material entity role
obsolete organism role
obsolete 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.
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
obsolete 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
obsolete 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.
healthcare facility
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
A community living health care facility in which patients receive health care by licensed nurses.
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 healthcare facility
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
obsolete identification process
obsolete 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 is one in which the patients are also residents of the facility.
long-term health care facility
long-term healthcare facility
community living healthcare facility
community living health care facility
A nurse role that requires successful completion of some nursing education program and some nursing license examination.
This class is intended to apply to registered nurse positions broadly, including those outside the US.
registered nurse role
A heatlh care encounter that occurs in a skilled nursing facility.
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 healthcare encounter
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 healthcare facility after receiving care
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 healthcare organization
home health care organization
home healthcare function
home health care function
A health care encounter that occurs in the housing unit where the patient resides.
home healthcare encounter
home health care encounter
obsolete questions asking process
palliative function
palliative care encounter
hospice organization
healthcare function
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.
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).
healthcare claim 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.
healthcare billing data set
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.
healthcare administrative process
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
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
John Beverley
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 health care organization
human role within a healthcare organization
Colbie Reed
institutional healthcare provider role
institutional health care provider role
A healthcare provider organization role that is realized by employing licensed nurses to deliver health care and assist with activities of daily living to patients in a skilled nursing facility.
skilled nursing role
An organization that is the bearer of a skilled nursing role.
skilled nursing organization
A time measurement data item that is measured in hours and is about the sum of the duration(s) of process(es) that realize a bearer's job role in a day.
number of hours per day of employment data item
An information content entity that is about whether someone is party to a marriage contract.
marital status
A marital status that is about a person who is party to a marriage contract.
married
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
S. Clint. Dowland
job role data item
income data item
government assistance healthcare plan data item
government assistance health care plan data item
healthcare 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 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 quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
A quality which inheres in a continuant.
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
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
Western Australian Mulga Shrublands Ecoregion
Australasia Ecoregion
Simpson Desert Region
Pilbara Shrublands Ecoregion
Carnarvon Xeric Shrublands Ecoregion
Central Ranges Xeric Shrub Ecoregion
Gibson Desert Ecoregion
The Great Sandy-Tanami Desert Ecoregion
Great Victoria Desert Ecoregion
Nullarbor Plains Xeric Shrubland Ecoregion
Afrotropical Ecoregion
Succulent Karoo Ecoregion
Arabian Peninsula: Yemen and Saudi Arabia
Yemen and Saudi Arabia Ecoregion
Arabian Peninsula: Yemen, Saudi Arabia, and Oman
Yemen, Saudi Arabia, and Oman Ecoregion
Somali montane xeric woodlands ecoregion
Somali Montane Xeric Woodland Ecoregion
Socotran Archipelago Ecoregion
Red Sea Coastal Desert Ecoregion
Namibian Savanna Woodland Ecoregion
Namib Desert Ecoregion
Nama Karoo Ecoregion
Masai Xeric Grasslands and Shrublands Ecoregion
Madagascar Succulent Woodlands Ecoregion
Madagascar Spiny Thickets Ecoregion
Africa: Coastal Namibia and Angola Ecoregion
Kaokoveld Desert Ecoregion
Kalahari Xeric Savanna Ecoregion
Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion
Ile Europa and Bassas da India Ecoregion
Hobyo Grassland and Shrubland Ecoregion
Arabian Peninsula: Oman and United Arab Emirates Ecoregion
Oman and United Arab Emirates Ecoregion
Ethiopian Xeric Grasslands and Shrublands Ecoregion
Eritrean Coastal Desert Ecoregion
North central Africa: Eastern Chad and small area of western Sudan
East Saharan Montane Xeric Woodland Ecoregion
Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion
Oman, Yemen, and Saudi Arabia Ecoregion
Aldabra Island Xeric Scrub Ecoregion
Indo-Malay Ecoregion
Thar Desert
Northwestern Thorn Scrub Forests
Solar radiation
example to be eventually removed
failed exploratory term
The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job.
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
Terms created as placeholders with the expectation of being permanent should instead be deprecated using the "placeholder removed" (obo:IAO_0000226) justification.
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
The term was created to ease viewing/sorting terms for development purposes, but 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
The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined.
This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider.
terms merged
The term has been combined with one or more other terms to create a more encompassing (merged) term.
An editor note should explain what were the merged terms and the reason for the merge.
The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge.
term imported
The term has been replaced by a term imported from another ontology.
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.
This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001.
term split
The term has been split into two or more new terms.
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 when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001.
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.
This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype.
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
Afaraf
Qafar af
Qafaraf
’Afar Af
Afar
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
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)
obsolete Afar
obsolete non-binary gender identity datum
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'
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).