Mark A. Miller
Hypertension Ontology For Clinical Data
2019-05-20
Amanda Hicks
Chris Stoeckert
Danielle Mowery
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
Person:Alan Ruttenberg
Really of interest to developers only
BFO CLIF specification label
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
example
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
example of usage
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
GROUP:OBI
OBI_0000277
in branch
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
OBI_0000281
has curation status
definition
definition
textual definition
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
definition
textual definition
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
editor note
editor note
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 http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor
definition editor
term editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
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
PERSON:Daniel Schober
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source
definition source
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.
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
has obsolescence reason
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
curator note
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
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
term tracker item
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'term requester' can credit the person, organization or project who request the ontology term.
ontology term requester
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
is denotator type
imported from
For external terms/classes, the ontology from which the term was imported
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
imported from
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 expression to
expand expression to
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.
Chris Mungall
expand assertion to
first order logic expression
An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.
PERSON:Alan Ruttenberg
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
Alan Ruttenberg
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:Alan Ruttenberg
PERSON:Bjoern Peters
PERSON:Chris Mungall
PERSON:Melanie Courtot
GROUP:OBO Foundry <http://obofoundry.org/>
OBO foundry unique label
obo foundry unique label
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 digit count
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
Person:Alan Ruttenberg
has ID range allocated to
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"
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
Person:Alan Ruttenberg
has ID policy for
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 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.
Person:Alan Ruttenberg
has ID prefix
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
elucidation
has associated axiom(nl)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(nl)
has associated axiom(fol)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom expressed in first order logic using CLIF syntax
has associated axiom(fol)
is allocated id range
Add as annotation triples in the granting ontology
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"
PERSON:Alan Ruttenberg
is allocated id range
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
Alan Ruttenberg
retired from use as of
has axiom id
Person:Alan Ruttenberg
Person:Alan Ruttenberg
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
Add as annotation triples in the granting ontology
Use on obsolete terms, relating the term to another term that can be used as a substitute
Person:Alan Ruttenberg
Person:Alan Ruttenberg
term replaced by
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
https://github.com/oborel/obo-relations/wiki/ROAndTime
tooth SubClassOf 'never in taxon' value 'Aves'
x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
Chris Mungall
?X DisjointWith RO_0002162 some ?Y
never in taxon
A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
non-overlapping with
shares no parts with
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
mutually spatially disjoint with
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
taxonomic class assertion
S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]
ambiguous for taxon
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
https://orcid.org/0000-0002-6601-2165
This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost
dubious for taxon
S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
https://orcid.org/0000-0002-6601-2165
present in taxon
defined by inverse
An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.
logical macro assertion
https://github.com/oborel/obo-relations/wiki/ShortcutRelations
An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N.
annotation property cardinality
A logical macro assertion whose domain is an IRI for a class
The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
logical macro assertion on a class
A logical macro assertion whose domain is an IRI for a property
logical macro assertion on a property
logical macro assertion on an object property
logical macro assertion on an annotation property
An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one.
dispositional interpretation
'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'
A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
shares no connection with
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))
has no connections with
inherited annotation property
Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)
curator guidance link
brain always_present_in_taxon 'Vertebrata'
forelimb always_present_in_taxon Euarchontoglires
S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S
This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed.
never lost in
always present in taxon
This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans.
temporal logical macro assertion on a class
measurement property has unit
has start time value
has end time value
Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property.
start, days post fertilization
Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property.
end, days post fertilization
Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1.
start, years post birth
Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2
end, years post birth
Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1.
start, months post birth
Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2
end, months post birth
Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in.
month of gestation
A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process
has developmental stage marker
Count of number of days intervening between the start of the stage and the time of coitum.
For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)
start, days post coitum
Count of number of days intervening between the end of the stage and the time of coitum.
end, days post coitum
start, weeks post birth
end, weeks post birth
If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p
is asymmetric relational form of process class
https://github.com/oborel/obo-relations/wiki/InteractionRelations
If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p
is symmetric relational form of process class
https://github.com/oborel/obo-relations/wiki/InteractionRelations
R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process
is relational form of process class
https://github.com/oborel/obo-relations/wiki/InteractionRelations
relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
The general property hierarchy is:
"directly P" SubPropertyOf "P"
Transitive(P)
Where we have an annotation assertion
"directly P" "is direct form of" "P"
If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
Chris Mungall
is direct form of
relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y
Chris Mungall
is indirect form of
logical macro assertion on an axiom
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
is a defining property chain axiom
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis.
is relational form of a class
A shortcut relationship that holds between two entities based on their identity criteria
logical macro assertion involving identity
A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds.
in approximate one to one relationship with
x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y
The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y"
is approximately equivalent to
'anterior end of organism' is-opposite-of 'posterior end of organism'
'increase in temperature' is-opposite-of 'decrease in temperature'
x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
is opposite of
x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
is indistinguishable from
evidential logical macro assertion on an axiom
A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom
This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
axiom has evidence
A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom
This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
axiom contradicted by evidence
In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context.
this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent.
If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion
is representative IRI for equivalence set
OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member
A metadata relation between a class and its taxonomic rank (eg species, family)
A metadata relation between a class and its taxonomic rank (eg species, family)
ncbi_taxonomy
This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored
This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored
has_rank
eco subset
Examples of a Contributor include a person, an
organisation, or a service. Typically, the name of a
Contributor should be used to indicate the entity.
An entity responsible for making contributions to the
content of the resource.
Contributor
Coverage will typically include spatial location (a place name
or geographic coordinates), temporal period (a period label,
date, or date range) or jurisdiction (such as a named
administrative entity).
Recommended best practice is to select a value from a
controlled vocabulary (for example, the Thesaurus of Geographic
Names [TGN]) and that, where appropriate, named places or time
periods be used in preference to numeric identifiers such as
sets of coordinates or date ranges.
The extent or scope of the content of the resource.
Coverage
Examples of a Creator include a person, an organisation,
or a service. Typically, the name of a Creator should
be used to indicate the entity.
An entity primarily responsible for making the content
of the resource.
Creator
Typically, Date will be associated with the creation or
availability of the resource. Recommended best practice
for encoding the date value is defined in a profile of
ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
A date associated with an event in the life cycle of the
resource.
Date
Description may include but is not limited to: an abstract,
table of contents, reference to a graphical representation
of content or a free-text account of the content.
An account of the content of the resource.
Description
Typically, Format may include the media-type or dimensions of
the resource. Format may be used to determine the software,
hardware or other equipment needed to display or operate the
resource. Examples of dimensions include size and duration.
Recommended best practice is to select a value from a
controlled vocabulary (for example, the list of Internet Media
Types [MIME] defining computer media formats).
The physical or digital manifestation of the resource.
Format
Recommended best practice is to identify the resource by means
of a string or number conforming to a formal identification
system.
Example formal identification systems include the Uniform
Resource Identifier (URI) (including the Uniform Resource
Locator (URL)), the Digital Object Identifier (DOI) and the
International Standard Book Number (ISBN).
An unambiguous reference to the resource within a given context.
Resource Identifier
Recommended best practice is to use RFC 3066 [RFC3066],
which, in conjunction with ISO 639 [ISO639], defines two-
and three-letter primary language tags with optional
subtags. Examples include "en" or "eng" for English,
"akk" for Akkadian, and "en-GB" for English used in the
United Kingdom.
A language of the intellectual content of the resource.
Language
Examples of a Publisher include a person, an organisation,
or a service.
Typically, the name of a Publisher should be used to
indicate the entity.
An entity responsible for making the resource available
Publisher
Recommended best practice is to reference the resource by means
of a string or number conforming to a formal identification
system.
A reference to a related resource.
Relation
Typically, a Rights element will contain a rights
management statement for the resource, or reference
a service providing such information. Rights information
often encompasses Intellectual Property Rights (IPR),
Copyright, and various Property Rights.
If the Rights element is absent, no assumptions can be made
about the status of these and other rights with respect to
the resource.
Information about rights held in and over the resource.
Rights Management
The present resource may be derived from the Source resource
in whole or in part. Recommended best practice is to reference
the resource by means of a string or number conforming to a
formal identification system.
A reference to a resource from which the present resource
is derived.
Source
Typically, a Subject will be expressed as keywords,
key phrases or classification codes that describe a topic
of the resource. Recommended best practice is to select
a value from a controlled vocabulary or formal
classification scheme.
The topic of the content of the resource.
Subject and Keywords
Typically, a Title will be a name by which the resource is
formally known.
A name given to the resource.
Title
Type includes terms describing general categories, functions,
genres, or aggregation levels for content. Recommended best
practice is to select a value from a controlled vocabulary
(for example, the DCMI Type Vocabulary [DCMITYPE]). To
describe the physical or digital manifestation of the
resource, use the Format element.
The nature or genre of the content of the resource.
Resource Type
subset_property
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
in_subset
shorthand
is defined by
is defined by
This is an experimental annotation
label
label
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
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
BFO:0000050
human_stages_ontology
part_of
part_of
part of
part of
http://www.obofoundry.org/ro/#OBO_REL: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
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.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent 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
BFO:0000051
protein
has_part
has_part
has part
has part
has_part
inheres in at all times
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
realized in
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL: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.
precedes
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
BFO:0000066
occurs_in
occurs_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
occurs in
occurs in
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
feature gives rise to disease
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
We will try to build it back up by elaborating the various subproperties that are more precisely defined.
Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
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.
denotes is 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
person:Alan Ruttenberg
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.
Alan Ruttenberg
is quality measurement of
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
Person:Alan Ruttenberg
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
Person:Alan Ruttenberg
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:Alan Ruttenberg
Person:Bjoern Peters
is quality specification of
inverse of the relation of is quality specification of
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
Person:Alan Ruttenberg
Person:Bjoern Peters
quality is specified as
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
Alan Ruttenberg
has time stamp
relates a time stamped measurement datum to the measurement datum that was measured
Alan Ruttenberg
has measurement datum
has_specified_input
see is_input_of example_of_usage
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
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
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Coutot
has_specified_input
has_specified_output
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.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
has_specified_output
has value specification
inheres in
this fragility inheres in this vase
this red color inheres in this apple
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
RO:0000052
inheres_in
inheres_in
inheres in
inheres in
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
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
http://www.obofoundry.org/ro/#OBO_REL:has_participant
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, 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).
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 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.
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
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 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
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
location_of
location of
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
Intended meaning:
domain: material entity
range: spatial region or site (immaterial continuant)
contained_in
contained in
contains
contains
penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)
A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
is allergic trigger for
A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
is autoimmune trigger for
penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)
A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
has allergic trigger
A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
has autoimmune trigger
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
located_in
http://www.obofoundry.org/ro/#OBO_REL:located_in
located in
located in
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
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.
David Osumi-Sutherland
has boundary
has_2D_boundary
has 2D boundary
The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).
David Osumi-Sutherland
tracheates
David Osumi-Sutherland
has synaptic terminal of
X outer_layer_of Y iff:
. X :continuant that bearer_of some PATO:laminar
. X part_of Y
. exists Z :surface
. X has_boundary Z
. Z boundary_of Y
has_boundary: http://purl.obolibrary.org/obo/RO_0002002
boundary_of: http://purl.obolibrary.org/obo/RO_0002000
David Osumi-Sutherland
A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
bounding layer of
A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
Note from NCEAS meeting: consider changing primary label
David Osumi-Sutherland
Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.
coincident with
x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
David Osumi-Sutherland
regulates in other organism
A part of relation that applies only between occurents.
occurent part of
David Osumi-Sutherland
<=
Primitive instance level timing relation between events
before or simultaneous with
David Osumi-Sutherland
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
simultaneous with
David Osumi-Sutherland
t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
before
David Osumi-Sutherland
Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which ends
David Osumi-Sutherland
di
Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
encompasses
David Osumi-Sutherland
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
David Osumi-Sutherland
starts_at_end_of
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
David Osumi-Sutherland
Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which starts
David Osumi-Sutherland
starts before
David Osumi-Sutherland
ends_at_start_of
meets
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
David Osumi-Sutherland
io
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts during
David Osumi-Sutherland
d
during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
happens during
David Osumi-Sutherland
o
overlaps
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
Relation between a neuron and an anatomical structure that its soma is part of.
David Osumi-Sutherland
<http://purl.obolibrary.org/obo/BFO_0000051> some (
<http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)
has soma location
relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
David Osumi-Sutherland
fasciculates with
(forall (?x ?y)
(iff
(fasciculates_with ?x ?y)
(exists (?nps ?npbs)
(and
("neuron ; CL_0000540" ?x)
("neuron projection bundle ; CARO_0001001" ?y)
("neuron projection segment ; CARO_0001502" ?nps)
("neuron projection bundle segment ; CARO_0001500' " ?npbs)
(part_of ?npbs ?y)
(part_of ?nps ?x)
(part_of ?nps ?npbs)
(forall (?npbss)
(if
(and
("neuron projection bundle subsegment ; CARO_0001501" ?npbss)
(part_of ?npbss ?npbs)
)
(overlaps ?nps ?npbss)
))))))
fasciculates with
Relation between a neuron and some structure its axon forms (chemical) synapses in.
Chris Mungall
David Osumi-Sutherland
David Osumi-Sutherland
<http://purl.obolibrary.org/obo/BFO_0000051> some (
<http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some (
<http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some (
<http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
axon synapses in
Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
Alexander Diehl
Chris Mungall
Lindsay Cowell
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)
has plasma membrane part
Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
Chris Mungall
David Osumi-Sutherland
synapsed in
http://purl.obolibrary.org/obo/BFO_0000051 some (
http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (
http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))
has postsynaptic terminal in
Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
synapses in
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
has presynaptic terminal in
Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
Chris Mungall
David Osumi-Sutherland
<http://purl.obolibrary.org/obo/BFO_0000051> some (
<http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some (
http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some (
<http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
dendrite synapsed in
A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
David Osumi-Sutherland
has synapse in
<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
has synaptic terminal in
x overlaps y if and only if there exists some z such that x has part z and z part of y
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
true
The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
David Osumi-Sutherland
has fasciculating component
(forall (?x ?y)
(iff
(has_fasciculating_neuron_projection ?x ?y)
(exists (?nps ?npbs)
(and
("neuron projection bundle ; CARO_0001001" ?x)
("neuron projection ; GO0043005" ?y)
("neuron projection segment ; CARO_0001502" ?nps)
("neuron projection bundle segment ; CARO_0001500" ?npbs)
(part_of ?nps ?y)
(part_of ?npbs ?x)
(part_of ?nps ?npbs)
(forall (?npbss)
(if
(and
("neuron projection bundle subsegment ; CARO_0001501" ?npbss)
(part_of ?npbss ?npbs)
)
(overlaps ?nps ?npbss)
))))))
has fasciculating neuron projection
X continuous_with Y if and only if X and Y share a fiat boundary.
David Osumi-Sutherland
connected to
The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
continuous with
FMA:85972
x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x
We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom
proper overlaps
(forall (?x ?y)
(iff
(proper_overlaps ?x ?y)
(and
(overlaps ?x ?y)
(not (part_of ?x ?y))
(not (part_of ?y ?x)))))
partially overlaps
A is spatially_disjoint_from B if and only if they have no parts in common
There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
Chris Mungall
Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
spatially disjoint from
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
connected to
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
The M8 connects Glasgow and Edinburgh
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
connects
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
supplies
Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
drains
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
A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
Chris Mungall
has phenotype
has phenotype
inverse of has phenotype
Chris Mungall
phenotype of
x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
Chris Mungall
David Hill
Tanya Berardini
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
regulates
x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y
Chris Mungall
negatively regulates (process to process)
negatively regulates
x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y
Chris Mungall
positively regulates (process to process)
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
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.
Chris Mungall
has function realized in
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)".
RO_0000053 some (RO_0000054 only ?Y)
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.
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.
Chris Mungall
has function in
RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))
capable of part of
true
x actively participates in y if and only if x participates in y and x realizes some active role
Chris Mungall
agent in
actively participates in
'heart development' has active participant some Shh protein
x has participant y if and only if x realizes some active role that inheres in y
This may be obsoleted and replaced by the original 'has agent' relation
Chris Mungall
has agent
has active participant
x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
Chris Mungall
surrounded by
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
This relation acts as a join point with BSPO
Chris Mungall
adjacent to
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
inverse of surrounded by
Chris Mungall
surrounds
Chris Mungall
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.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
inverse of starts with
Chris Mungall
Allen
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.
Chris Mungall
started by
starts with
inverse of ends with
Chris Mungall
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.
Chris Mungall
finished by
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
Chris Mungall
starts with process that occurs in
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
Chris Mungall
ends with process that occurs in
has end location
p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
Chris Mungall
consumes
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
Chris Mungall
produces
has output
A broad relationship between an exposure event or process and any entity (e.g., a human, human population, or a human organ) that interacts with an exposure stressor during the exposure event
ExO:0000001
has exposure receptor
A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event.
ExO:0000000
has exposure stressor
A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor
ExO:0000055
has exposure route
A broad relationship between an exposure event or process and a the material an agent takes from the source to the target.
has exposure transport path
related via exposure to
Any portion of roundup 'has active ingredient' some glyphosate
A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.
has active substance
has active pharmaceutical ingredient
has active ingredient
inverse of has active ingredient
active ingredient in'
b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.
connecting branch of
inverse of connecting branch of
has connecting branch
c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)
has biological role
c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)
has application role
c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)
has chemical role
c involved in regulation of p if c enables 'p' and p' causally upstream of p
acts upstream of
c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p
affects
acts upstream of or within
Inverse of 'is substance that treats'
cjm
is treated by substance
cjm
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
causally upstream of, positive effect
cjm
holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
causally upstream of, negative effect
q inheres in 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 inheres in part of
Chris Mungall
RO:0002314
inheres_in_part_of
inheres_in_part_of
inheres in part of
inheres in part of
true
A mereological relationship or a topological relationship
A mereological relationship or a topological relationship
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
Chris Mungall
http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with
In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
Gene Ontology Consortium
colocalizes with
ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
We would like to say
if and only if
exists c', p'
c part_of c' and c' capable_of p
and
c capable_of p' and p' part_of p
then
c contributes_to p
However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
Chris Mungall
http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to
In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
contributes to
a particular instances of akt-2 enables some instance of protein kinase activity
Chris Mungall
catalyzes
executes
has
is catalyzing
is executing
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.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
Chris Mungall
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.
Chris Mungall
false
part of structure that is capable of
true
c involved_in p if and only if c enables some process p', and p' is part of p
Chris Mungall
actively involved in
enables part of
involved in
every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
p regulates levels of c if p regulates some amount (PATO:0000070) of c
Chris Mungall
regulates levels of (process to entity)
regulates levels of
inverse of enables
Chris Mungall
enabled by
inverse of regulates
Chris Mungall
regulated by (processual)
regulated by
inverse of negatively regulates
Chris Mungall
negatively regulated by
inverse of positively regulates
Chris Mungall
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.
is member of
member part of
SIO
member of
has member is a mereological relation between a collection and an item.
SIO
has member
inverse of has input
Chris Mungall
input of
inverse of has output
Chris Mungall
output of
Chris Mungall
formed as result of
Chris Mungall
http://neurolex.org/wiki/Property:DendriteLocation
has dendrite location
A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)
in branching relationship with
https://github.com/obophenotype/uberon/issues/170
Deschutes River tributary_of Columbia River
inferior epigastric vein tributary_of external iliac vein
x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
Chris Mungall
drains into
drains to
tributary channel of
http://en.wikipedia.org/wiki/Tributary
http://www.medindia.net/glossary/venous_tributary.htm
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
tributary of
http://en.wikipedia.org/wiki/Tributary
Deschutes River distributary_of Little Lava Lake
x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x
Chris Mungall
branch of
distributary channel of
http://en.wikipedia.org/wiki/Distributary
This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes
distributary of
x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y.
Chris Mungall
anastomoses with
anabranch of
A lump of clay and a statue
x spatially_coextensive_with y if and inly if x and y have the same location
Chris Mungall
This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
spatially coextensive with
x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
Chris Mungall
branching part of
FMA:85994
x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path.
Chris Mungall
main stem of
x proper_distributary_of y iff x distributary_of y and x does not flow back into y
Chris Mungall
proper distributary of
x proper_tributary_of y iff x tributary_of y and x does not originate from y
Chris Mungall
proper tributary of
'protein catabolic process' SubClassOf has_direct_input some protein
p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
Chris Mungall
directly consumes
This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'
has direct input
Chris Mungall
Likely to be obsoleted. See:
https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
obsolete has indirect output
true
inverse of upstream of
Chris Mungall
causally downstream of
Chris Mungall
immediately causally downstream of
p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
Chris Mungall
directly positively regulates
directly activates (process to process)
directly activates
p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
Chris Mungall
indirectly positively regulates
indirectly activates
Chris Mungall
directly negatively regulates
directly inhibits (process to process)
directly inhibits
Chris Mungall
indirectly negatively regulates
indirectly inhibits
This relation groups causal relations between material entities and causal relations between processes
This relation groups causal relations between material entities and causal relations between processes
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.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
Chris Mungall
causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
Chris Mungall
immediately causally upstream of
p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit
Chris Mungall
directly provides input for (process to process)
directly provides input for
transitive form of directly_provides_input_for
Chris Mungall
This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')
transitively provides input for (process to process)
transitively provides input for
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
Chris Mungall
influences (processual)
affects
causally upstream of or within
inverse of causally upstream of or within
Chris Mungall
causally downstream of or within
c involved in regulation of p if c is involved in some 'p' and p' regulates some p
Chris Mungall
involved in regulation of
Chris Mungall
involved in positive regulation of
Chris Mungall
involved in negative regulation of
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
Chris Mungall
involved in or reguates
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
Chris Mungall
executes activity in
enables activity in
true
p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
Chris Mungall
contributes to morphology of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
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.
Chris Mungall
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.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/MI_0914
https://github.com/oborel/obo-relations/wiki/InteractionRelations
Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b
Chris Mungall
molecularly controls
Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b.
Chris Mungall
inhibits
molecularly decreases activity of
Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b.
Chris Mungall
activates
molecularly increases activity of
A relation that holds between a disease or an organism and a phenotype
Chris Mungall
has symptom
Chris Mungall
Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target
partner in
Chris Mungall
Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed.
subject participant in
Chris Mungall
Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed.
target participant in
A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and
the a supports either the existence of b, or the truth value of b.
Chris Mungall
is evidence for
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
Chris Mungall
composed primarily of
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.
Chris Mungall
has part that occurs in
true
See notes for inverse relation
Chris Mungall
receives input from
This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.
Chris Mungall
sends output to
A relationship between a material entity and a process where the material entity has some causal role that influences the process
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
Chris Mungall
depends on
depends_on
q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
Chris Mungall
towards
'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate
p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c
Chris Mungall
has intermediate product
has intermediate
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
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between material entities
A coral reef environment is determined by a particular coral reef
s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
Chris Mungall
determined by (system to material entity)
Chris Mungall
Pier Buttigieg
determined by
inverse of determined by
Chris Mungall
determines (material entity to system)
determines
s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
Chris Mungall
determined by part of
true
A relation that holds between two entities that have the property of being sequences or having sequences.
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect.
The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene.
sequentially related to
Every UTR is adjacent to a CDS of the same transcript
Two consecutive DNA residues are sequentially adjacent
Two exons on a processed transcript that were previously connected by an intron are adjacent
x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
sequentially adjacent to
Every CDS has as a start sequence the start codon for that transcript
x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence
Chris Mungall
started by
http://www.ncbi.nlm.nih.gov/pubmed/20226267
has start sequence
inverse of has start sequence
Chris Mungall
starts
http://www.ncbi.nlm.nih.gov/pubmed/20226267
is start sequence of
Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)
x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence
Chris Mungall
ended by
http://www.ncbi.nlm.nih.gov/pubmed/20226267
has end sequence
inverse of has end sequence
Chris Mungall
ends
http://www.ncbi.nlm.nih.gov/pubmed/20226267
is end sequence of
x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y.
In the SO paper, this was defined as an instance-type relation
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
is consecutive sequence of
Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence.
x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering
Chris Mungall
is sequentially aligned with
The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)
x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y
Chris Mungall
bounds sequence of
inverse of bounds sequence of
Chris Mungall
is bound by sequence of
x has subsequence y iff all of the sequence parts of x are sequence parts of y
Chris Mungall
contains
http://www.ncbi.nlm.nih.gov/pubmed/20226267
has subsequence
inverse of has subsequence
Chris Mungall
contained by
is subsequence of
x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.
Chris Mungall
overlaps sequence of
x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y.
Chris Mungall
disconnected from
does not overlap sequence of
inverse of downstream of sequence of
Chris Mungall
is upstream of sequence of
x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.
Chris Mungall
is downstream of sequence of
A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript
x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y
Chris Mungall
is immediately downstream of sequence of
A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript
inverse of immediately downstream of
Chris Mungall
is immediately upstream of sequence of
Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.
Chris Mungall
has supporting framework
The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).
has skeleton
inverse of is evidence for
Chris Mungall
x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x.
has evidence
Chris Mungall
causally influenced by (material entity to material entity)
causally influenced by
Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
Chris Mungall
results in movement of
Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b
Chris Mungall
causally influences (material entity to material entity)
causally influences
inverse of branching part of
Chris Mungall
has branching part
x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.
Chris Mungall
UBERON:cjm
This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.
conduit for
x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
Chris Mungall
GOC:cjm
lumen of
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
Chris Mungall
luminal space of
A relation that holds between an attribute or a qualifier and another attribute.
Chris Mungall
This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are.
RO:0002180
qualifier
qualifier
placeholder relation to indicate normality/abnormality.
has modifier
inverse of has skeleton
Chris Mungall
skeleton of
p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p
Chris Mungall
directly regulates (processual)
directly regulates
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
Chris Mungall
has part structure that is capable of
p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p
results in breakdown of
p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released.
results in catabolism of
results in disassembly of
results in remodeling of
p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c
results in organization of
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.
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.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
Chris Mungall
causal relation between material entity and a process
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
capable of negatively regulating
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.
capable of positively regulating
pazopanib -> pathological angiogenesis
Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p.
treats
The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber.
capable of inhibiting or preventing pathological process
treats
Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship
benzene -> cancer [CHEBI]
Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p.
causes disease
capable of upregulating or causing pathological process
c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d.
treats
is substance that treats
c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d.
May be ceded to OBI
is marker for
Inverse of 'causal agent in'
has causal agent
A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
related via dependence to
An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support.
A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.
In the Gene Ontology association model, this corresponds to the With/From field
is evidence with support from
related via evidence or inference to
p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p
directly positively regulates (process to process)
directly positively regulates
p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p
directly negatively regulates (process to process)
directly negatively regulates
Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b.
Logical axioms to be added after the relevant branch of GO is MIREOTed in
represses expression of
Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b.
Logical axioms to be added after the relevant branch of GO is MIREOTed in
increases expression of
The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.
An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.
A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition.
Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.
Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.
Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions.
causes or contributes to condition
A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition.
causes condition
A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition.
contributes to condition
A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual.
contributes to expressivity of condition
contributes to severity of condition
A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population.
contributes to penetrance of condition
contributes to frequency of condition
A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition.
Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.
Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions.
is preventative for condition
A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.
correlated with condition
A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature.
disease arises from feature
has phenotype affecting
AG: Currently the only way to handle relational quality?
relation binding a relational quality or disposition to the relevant type of entity
towards
has measurement value
has x coordinate value
has z coordinate value
has y coordinate value
entity
Entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
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
per discussion with Barry Smith
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
Continuant
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.
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
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]
occurrent
Occurrent
An entity that has temporal parts and that happens, unfolds or develops through time.
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
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.
per discussion with Barry Smith
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]
ic
IndependentContinuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
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]
s-region
SpatialRegion
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
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.
per discussion with Barry Smith
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]
t-region
TemporalRegion
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
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
per discussion with Barry Smith
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]
2d-s-region
TwoDimensionalSpatialRegion
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
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]
st-region
SpatiotemporalRegion
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 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 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]
process
Process
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
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
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])
(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]
disposition
Disposition
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
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]
realizable
RealizableEntity
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
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]
0d-s-region
ZeroDimensionalSpatialRegion
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
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]
quality
Quality
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]
bfo
BFO:0000019
quality
quality
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]
sdc
SpecificallyDependentContinuant
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 role of being a doctor
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.
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
specifically dependent continuant
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.
per discussion with Barry Smith
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
role
Role
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a 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
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]
fiat-object-part
FiatObjectPart
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]
bfo
BFO:0000024
fiat object part
fiat object part
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]
1d-s-region
OneDimensionalSpatialRegion
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 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]
object-aggregate
ObjectAggregate
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
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
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]
3d-s-region
ThreeDimensionalSpatialRegion
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
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]
site
Site
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
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]
object
Object
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])
bfo
BFO:0000030
object
object
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])
gdc
GenericallyDependentContinuant
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
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]
function
Function
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
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]
p-boundary
ProcessBoundary
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
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]
1d-t-region
OneDimensionalTemporalRegion
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 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]
material
MaterialEntity
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.
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
bfo
BFO:0000040
material entity
material entity
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]
cf-boundary
ContinuantFiatBoundary
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
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])
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.
(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]
immaterial
ImmaterialEntity
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
1d-cf-boundary
OneDimensionalContinuantFiatBoundary
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
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]
process-profile
ProcessProfile
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
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]
r-quality
RelationalQuality
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.
a marriage bond, an instance of 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
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]
2d-cf-boundary
TwoDimensionalContinuantFiatBoundary
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
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]
0d-cf-boundary
ZeroDimensionalContinuantFiatBoundary
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
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.
requested by Melanie Courtot
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]
0d-t-region
ZeroDimensionalTemporalRegion
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 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]
history
History
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
immaterial anatomical entity
biological entity
A disease that involving errors in metabolic processes of building or degradation of molecules.
ICD10CM:E88.9
ICD9CM:277.9
MESH:D008659
NCI:C3235
SNOMEDCT_US_2016_03_01:154733004
SNOMEDCT_US_2016_03_01:190961002
SNOMEDCT_US_2016_03_01:267456000
SNOMEDCT_US_2016_03_01:30390004
SNOMEDCT_US_2016_03_01:75934005
UMLS_CUI:C0025517
metabolic disease
disease_ontology
DOID:0014667
disease of metabolism
An acquired metabolic disease that is characterized by abnormal carbohydrate metabolism.
disease_ontology
DOID:0050013
carbohydrate metabolism disease
A disease that is the consequence of the presence of pathogenic microbial agents, including pathogenic viruses, pathogenic bacteria, fungi, protozoa, multicellular parasites, and aberrant proteins known as prions.
DOID:10115
DOID:11078
DOID:1304
DOID:1321
DOID:2040
DOID:2288
DOID:3099
DOID:4120
DOID:4620
DOID:5256
DOID:945
DOID:95
DOID:9532
DOID:9696
ICD9CM:079.0
UMLS_CUI:C0001485
infectious disease
disease_ontology
DOID:0050117
disease by infectious agent
A bacterial pneumonia which is an acute pulmonary inflammatory response that develops after the inhalation of colonized oropharyngeal material containing bacteria. It is seen in individuals with dysphagia and gastric dysmotility. The disease has_symptom tachypnea and has_symptom cough.
ICD10CM:J69.0
MESH:D011015
SNOMEDCT_US_2016_03_01:422588002
SNOMEDCT_US_2016_03_01:47839005
UMLS_CUI:C0032290
disease_ontology
DOID:0050152
aspiration pneumonia
A nervous system disease which is located in a part of the nervous system responsible for processing sensory information that consists of sensory receptors, neural pathways, and parts of the brain involved in sensory perception. Commonly recognized sensory systems are those for vision, hearing, somatic sensation (touch), taste and olfaction (smell).
disease_ontology
DOID:0050155
sensory system disease
A respiratory system disease which involves the lower respiratory tract.
ICD9CM:478.1
ICD9CM:478.19
SNOMEDCT_US_2016_03_01:195823002
SNOMEDCT_US_2016_03_01:266346007
UMLS_CUI:C0029581
disease_ontology
DOID:0050161
lower respiratory tract disease
A genetic disease that is the result of one or more abnormal alleles and may be dominant (a single copy of the abnormal allele is sufficient to give rise to the disease), semi-dominant, or recessive (requiring both copies of the gene to have an abnormal allele).
disease_ontology
DOID:0050177
monogenic disease
An organ system cancer located_in the respiratory system that is characterized by uncontrolled cellular proliferation in the respiratory tract.
disease_ontology
DOID:0050615
respiratory system cancer
An organ system benign neoplasm that is located_in reproductive system organs.
disease_ontology
DOID:0050622
reproductive organ benign neoplasm
A cancer that is classified based on the organ it starts in.
snadendla
2011-06-13T03:28:33Z
MESH:D009371
disease_ontology
DOID:0050686
organ system cancer
A cancer that is classified by the type of cell from which it is derived.
snadendla
2011-06-13T03:28:50Z
disease_ontology
DOID:0050687
cell type cancer
A heart disease and a myopathy that is characterized by deterioration of the function of the heart muscle.
lschriml
2012-01-03T02:54:11Z
ICD10CM:I42
ICD10CM:I42.9
ICD10CM:I51.5
ICD9CM:425
ICD9CM:425.9
MESH:D009202
NCI:C34830
NCI:C53654
SNOMEDCT_US_2016_03_01:155351008
SNOMEDCT_US_2016_03_01:155353006
SNOMEDCT_US_2016_03_01:195035002
SNOMEDCT_US_2016_03_01:195037005
SNOMEDCT_US_2016_03_01:20072003
SNOMEDCT_US_2016_03_01:266244008
SNOMEDCT_US_2016_03_01:266301006
SNOMEDCT_US_2016_03_01:57809008
SNOMEDCT_US_2016_03_01:85898001
SNOMEDCT_US_2016_03_01:89461002
SNOMEDCT_US_2016_03_01:89600009
UMLS_CUI:C0033141
UMLS_CUI:C0036529
UMLS_CUI:C0878544
Cardiomyopathies
disease_ontology
DOID:0050700
MESH:D009202 added from NeuroDevNet [WAK].
cardiomyopathy
An autosomal genetic disease that is characterized by the presence of one disease-associated mutation of a gene which is sufficient to cause the disease.
lschriml
2012-07-24T12:51:47Z
disease_ontology
DOID:0050736
autosomal dominant disease
A monogenic disease that is has material basis in a mutation in a single gene on one of the non-sex chromosomes.
lschriml
2012-07-24T04:45:53Z
disease_ontology
DOID:0050739
autosomal genetic disease
An acquired metabolic disease that characterized by excessive production of acid.
lschriml
2013-01-16T01:23:37Z
disease_ontology
DOID:0050758
metabolic acidosis
A vascular disease that is located_in an artery.
lschriml
2014-02-12T03:08:35Z
disease_ontology
DOID:0050828
artery disease
A glomerulonephritis that is characterized by hardening of the glomerulus in the kidney.
lschriml
2014-04-15T03:40:31Z
disease_ontology
DOID:0050851
glomerulosclerosis
lschriml
2014-06-25T05:14:03Z
disease_ontology
DOID:0050871
fibroma
A cardiomyopathy that is characterized as weakness in the muscle of the heart that is not due to an identifiable external cause.
disease_ontology
DOID:0060036
intrinsic cardiomyopathy
A disease of mental health that involves the impairment in normal sexual functioning.
disease_ontology
DOID:0060043
sexual disorder
A disease of cellular proliferation that results in abnormal growths in the body which lack the ability to metastasize.
lschriml
2011-05-11T12:18:41Z
disease_ontology
DOID:0060072
benign neoplasm
A benign neoplasm that is classified by the type of cell or tissue from which it is derived.
lschriml
2011-07-14T11:59:48Z
disease_ontology
DOID:0060084
cell type benign neoplasm
A benign neoplasm that is classified by the organ system from which it is arising from.
lschriml
2011-07-14T12:12:23Z
disease_ontology
DOID:0060085
organ system benign neoplasm
lschriml
2011-07-14T12:20:52Z
disease_ontology
DOID:0060086
female reproductive organ benign neoplasm
lschriml
2011-07-15T01:42:11Z
DOID:0060113
disease_ontology
DOID:0060095
uterine benign neoplasm
A disease of metabolism that has _material_basis_in enzyme deficiency or accumulation of enzymes or toxins which interfere with normal function due to an endocrine organ disease, organ malfunction, inadequate intake, dietary deficiency, or malabsorption.
lschriml
2011-08-24T02:53:03Z
disease_ontology
DOID:0060158
acquired metabolic disease
A congestive heart failure characterized by a sudden stop in effective blood circulation due to the failure of the heart to contract effectively or at all.
emitraka
2015-02-25T15:12:30Z
ICD10CM:I46
ICD9CM:427.5
MESH:D006323
NCI:C50479
NCI:C50483
SNOMEDCT_US_2016_03_01:155372006
SNOMEDCT_US_2016_03_01:195085006
SNOMEDCT_US_2016_03_01:195090009
SNOMEDCT_US_2016_03_01:233926006
SNOMEDCT_US_2016_03_01:251189000
SNOMEDCT_US_2016_03_01:30298009
SNOMEDCT_US_2016_03_01:309810002
SNOMEDCT_US_2016_03_01:397829000
SNOMEDCT_US_2016_03_01:397912004
SNOMEDCT_US_2016_03_01:410429000
SNOMEDCT_US_2016_03_01:410430005
UMLS_CUI:C0018790
UMLS_CUI:C0600228
cardiopulmonary arrest
circulatory arrest
disease_ontology
DOID:0060319
cardiac arrest
ICD10CM:I44.60
ICD9CM:426.2
SNOMEDCT_US_2016_03_01:195044001
SNOMEDCT_US_2016_03_01:195045000
SNOMEDCT_US_2016_03_01:266245009
SNOMEDCT_US_2016_03_01:4973001
UMLS_CUI:C0155702
Left bundle branch [block] or [hemiblock]
Left bundle branch hemiblock (disorder)
Left bundle branch hemiblock NOS (disorder)
disease_ontology
DOID:10272
left bundle branch hemiblock
A cardiovascular system disease that involves the heart's electrical conduction system.
ICD9CM:426.6
SNOMEDCT_US_2016_03_01:195053008
SNOMEDCT_US_2016_03_01:195056000
UMLS_CUI:C0029630
heart rhythm disease
disease_ontology
DOID:10273
heart conduction disease
A disease by infectious agent that results_in infection, has_material_basis_in Bacteria.
ICD10CM:A49
ICD10CM:A49.9
MESH:D001424
MESH:D016905
MESH:D016908
NCI:C2890
SNOMEDCT_US_2016_03_01:154318005
SNOMEDCT_US_2016_03_01:186470002
SNOMEDCT_US_2016_03_01:187347000
SNOMEDCT_US_2016_03_01:266182006
SNOMEDCT_US_2016_03_01:266187000
SNOMEDCT_US_2016_03_01:301811001
SNOMEDCT_US_2016_03_01:87628006
UMLS_CUI:C0004623
disease_ontology
DOID:104
bacterial infectious disease
A hypertension occurring during pregnancy characterized by large amounts of protein in the urine (proteinuria) and edema, usually by the last trimester of pregnancy.
DOID:12684
ICD10CM:O14
ICD10CM:O14.9
ICD10CM:O14.90
MESH:D011225
NCI:C34943
NCI:C85021
OMIM:189800
OMIM:609402
OMIM:609403
OMIM:609404
OMIM:614592
ORDO:275555
SNOMEDCT_US_2016_03_01:15394000
SNOMEDCT_US_2016_03_01:156106005
SNOMEDCT_US_2016_03_01:156109003
SNOMEDCT_US_2016_03_01:198972006
SNOMEDCT_US_2016_03_01:198979002
SNOMEDCT_US_2016_03_01:199011002
SNOMEDCT_US_2016_03_01:237280005
SNOMEDCT_US_2016_03_01:267306006
SNOMEDCT_US_2016_03_01:288201007
SNOMEDCT_US_2016_03_01:398254007
SNOMEDCT_US_2016_03_01:46764007
SNOMEDCT_US_2016_03_01:6758009
UMLS_CUI:C0032914
gestational hypertension
hypertension induced by pregnancy
pre-eclamptic toxaemia
preeclampsia
preeclampsia/eclampsia
pregnancy associated hypertension
pregnancy toxemia
proteinuric hypertension of pregnancy
toxaemia of pregnancy
disease_ontology
DOID:10591
Xref MGI.
OMIM mapping confirmed by DO. [SN].
pre-eclampsia
MESH:D006977
NCI:C3121
SNOMEDCT_US_2016_03_01:194775007
SNOMEDCT_US_2016_03_01:28119000
UMLS_CUI:C0020544
disease_ontology
DOID:1073
renal hypertension
A kidney disease characterized by the failure of the kidneys to adequately filter waste products from the blood.
ICD10CM:N19
ICD9CM:586
MESH:D051437
NCI:C4376
SNOMEDCT_US_2016_03_01:156092003
SNOMEDCT_US_2016_03_01:197656003
SNOMEDCT_US_2016_03_01:198524000
SNOMEDCT_US_2016_03_01:266553002
SNOMEDCT_US_2016_03_01:266616000
SNOMEDCT_US_2016_03_01:42399005
UMLS_CUI:C0035078
renal failure
disease_ontology
DOID:1074
PRISM.
kidney failure
ICD10CM:N11
ICD10CM:N11.9
ICD9CM:590.0
NCI:C123216
SNOMEDCT_US_2016_03_01:123293005
SNOMEDCT_US_2016_03_01:155861006
SNOMEDCT_US_2016_03_01:197767009
SNOMEDCT_US_2016_03_01:266619007
SNOMEDCT_US_2016_03_01:63302006
UMLS_CUI:C0085697
disease_ontology
DOID:1076
chronic pyelonephritis
An artery disease characterized by chronic elevated blood pressure in the arteries.
EFO:0000537
ICD10CM:I10
ICD10CM:I10-I15
ICD9CM:401-405.99
ICD9CM:997.91
MESH:D006973
NCI:C3117
SNOMEDCT_US_2016_03_01:155295004
SNOMEDCT_US_2016_03_01:155302005
SNOMEDCT_US_2016_03_01:194756002
SNOMEDCT_US_2016_03_01:194757006
SNOMEDCT_US_2016_03_01:194760004
SNOMEDCT_US_2016_03_01:194794002
SNOMEDCT_US_2016_03_01:195537001
SNOMEDCT_US_2016_03_01:266287006
SNOMEDCT_US_2016_03_01:38341003
UMLS_CUI:C0020538
HTN
High blood pressure (& [essential hypertension])
hyperpiesia
vascular hypertensive disorder
disease_ontology
hypertensive disease
DOID:10763
hypertension
ICD10CM:M31.1
MESH:D011697
NCI:C78797
SNOMEDCT_US_2016_03_01:155443009
SNOMEDCT_US_2016_03_01:195358008
SNOMEDCT_US_2016_03_01:195359000
SNOMEDCT_US_2016_03_01:360402008
SNOMEDCT_US_2016_03_01:78129009
UMLS_CUI:C0034155
Moschcowitz's syndrome
disease_ontology
DOID:10772
thrombotic thrombocytopenic purpura
A hypertension with no known cause. It is the most common type of hypertension.
ICD10CM:I10
ICD9CM:401
ICD9CM:401.9
MESH:C562386
NCI:C3478
OMIM:145500
OMIM:603918
OMIM:604329
OMIM:607329
OMIM:608742
OMIM:610261
OMIM:610262
OMIM:610948
OMIM:611014
ORDO:243761
SNOMEDCT_US_2016_03_01:155296003
SNOMEDCT_US_2016_03_01:194757006
SNOMEDCT_US_2016_03_01:194760004
SNOMEDCT_US_2016_03_01:266228004
SNOMEDCT_US_2016_03_01:59621000
UMLS_CUI:C0085580
idiopathic hypertension
primary hypertension
disease_ontology
DOID:10825
Xref MGI.
OMIM mapping confirmed by DO. [SN].
essential hypertension
ICD10CM:H49.2
ICD9CM:378.54
MESH:D020434
NCI:C27592
NCI:C27593
OMIM:100200
SNOMEDCT_US_2016_03_01:14720007
SNOMEDCT_US_2016_03_01:230533001
SNOMEDCT_US_2016_03_01:398760006
SNOMEDCT_US_2016_03_01:398925009
SNOMEDCT_US_2016_03_01:398963001
SNOMEDCT_US_2016_03_01:46587002
SNOMEDCT_US_2016_03_01:4892003
SNOMEDCT_US_2016_03_01:82373004
UMLS_CUI:C0271355
Abducens nerve disorder
Abducens nerve weakness
Lateral rectus muscle denervation paresis
Lateral rectus muscle innervation disorder
Sixth cranial nerve disorder, NOS
Sixth nerve palsy (disorder)
Sixth or abducens nerve palsy
VIth nerve Paralysis
VIth nerve disorder
disorder of abducent nerve
disease_ontology
DOID:10865
abducens nerve disease
A cerebral degeneration characterized by an abnormal accumulation of cerebrospinal fluid in the ventricles of the brain, leading to progressive enlargement of the head.
ICD10CM:G91
ICD10CM:G91.9
MESH:D006849
NCI:C3111
OMIM:123155
OMIM:236600
OMIM:236635
OMIM:307000
OMIM:615219
ORDO:2182
ORDO:2185
SNOMEDCT_US_2016_03_01:154995000
SNOMEDCT_US_2016_03_01:154997008
SNOMEDCT_US_2016_03_01:192807008
SNOMEDCT_US_2016_03_01:230745008
SNOMEDCT_US_2016_03_01:267687006
UMLS_CUI:C0020255
hydrocephalus, X-linked
hydrocephalus, nonsyndromic, autosomal recessive
disease_ontology
DOID:10908
Xref MGI.
OMIM mapping confirmed by DO. [SN].
hydrocephalus
ICD10CM:K14
ICD10CM:K14.9
ICD9CM:529.9
MESH:D014060
SNOMEDCT_US_2016_03_01:155533008
SNOMEDCT_US_2016_03_01:155665004
SNOMEDCT_US_2016_03_01:155667007
SNOMEDCT_US_2016_03_01:196595001
SNOMEDCT_US_2016_03_01:266496009
SNOMEDCT_US_2016_03_01:69244009
UMLS_CUI:C0040409
disease_ontology
DOID:10944
tongue disease
A kidney disease that is characterized by an inflammation of the kidneys.
ICD10CM:N05
ICD10CM:N08
MESH:D009393
NCI:C26833
SNOMEDCT_US_2016_03_01:155853001
SNOMEDCT_US_2016_03_01:266615001
SNOMEDCT_US_2016_03_01:274107001
SNOMEDCT_US_2016_03_01:52845002
UMLS_CUI:C0027697
disease_ontology
DOID:10952
nephritis
ICD10CM:I15
ICD10CM:I15.9
ICD9CM:405
ICD9CM:405.9
NCI:C3657
SNOMEDCT_US_2016_03_01:155300002
SNOMEDCT_US_2016_03_01:194789002
SNOMEDCT_US_2016_03_01:194792003
SNOMEDCT_US_2016_03_01:31992008
UMLS_CUI:C0155616
disease_ontology
DOID:11130
secondary hypertension
A lung disease characterized by inadequate gas exchange by the respiratory system.
DOID:11391
DOID:11392
DOID:11393
ICD10CM:J96.0
ICD9CM:518.81
NCI:C27043
SNOMEDCT_US_2016_03_01:65710008
UMLS_CUI:C0264490
acute and chronic respiratory failure
acute respiratory Failure
acute-on-chronic respiratory failure
chronic respiratory failure
respiratory insufficiency/failure
disease_ontology
DOID:11162
respiratory failure
ICD10CM:D65
ICD9CM:286.6
MESH:D004211
NCI:C2992
SNOMEDCT_US_2016_03_01:267563002
SNOMEDCT_US_2016_03_01:67406007
UMLS_CUI:C0012739
DIC
Defibrination syndrome
Diffuse or disseminated intravascular coagulation
disease_ontology
DOID:11247
disseminated intravascular coagulation
DOID:13472
ICD10CM:J81
ICD10CM:J81.1
MESH:D011654
NCI:C26868
SNOMEDCT_US_2016_03_01:19242006
SNOMEDCT_US_2016_03_01:196119001
SNOMEDCT_US_2016_03_01:266408001
UMLS_CUI:C0034063
disease_ontology
DOID:11396
pulmonary edema
A cardiovascular system disease that involves the heart.
ICD10CM:I51.9
ICD9CM:429.9
MESH:D006331
NCI:C3079
SNOMEDCT_US_2016_03_01:155263000
SNOMEDCT_US_2016_03_01:194707003
SNOMEDCT_US_2016_03_01:195152001
SNOMEDCT_US_2016_03_01:266275004
SNOMEDCT_US_2016_03_01:266311004
SNOMEDCT_US_2016_03_01:56265001
UMLS_CUI:C0018799
disease_ontology
DOID:114
heart disease
ICD10CM:N10-N16
ICD10CM:N12
ICD10CM:N16
ICD9CM:590.80
MESH:D011704
NCI:C34965
SNOMEDCT_US_2016_03_01:197779009
SNOMEDCT_US_2016_03_01:197784003
SNOMEDCT_US_2016_03_01:45816000
UMLS_CUI:C0034186
disease_ontology
DOID:11400
pyelonephritis
ICD10CM:G93.2
ICD9CM:348.2
MESH:D011559
NCI:C85035
OMIM:243200
SNOMEDCT_US_2016_03_01:155052007
SNOMEDCT_US_2016_03_01:267701004
SNOMEDCT_US_2016_03_01:68267002
UMLS_CUI:C0033845
Pseudotumor cerebri
benign intracran. hypt.
benign intracranial hypertension
benign intracranial hypertension (disorder)
idiopathic intracranial hypertension
disease_ontology
DOID:11459
OMIM mapping confirmed by DO. [SN].
pseudotumor cerebri
ICD9CM:337.1
UMLS_CUI:C0154691
autonomic nervous system disorder
disease_ontology
DOID:11465
autonomic nervous system disease
DOID:11737
DOID:13947
ICD10CM:Q23.3
ICD9CM:396.3
ICD9CM:746.6
MESH:D008944
NCI:C50852
NCI:C50888
SNOMEDCT_US_2016_03_01:194736003
SNOMEDCT_US_2016_03_01:194977007
SNOMEDCT_US_2016_03_01:233857005
SNOMEDCT_US_2016_03_01:29928006
SNOMEDCT_US_2016_03_01:48724000
UMLS_CUI:C0026266
UMLS_CUI:C0158619
UMLS_CUI:C0264774
Congenital insufficiency of mitral valve (disorder)
Mitral valve incompetence
congenital mitral insufficiency
congenital mitral regurgitation
mitral regurgitation
disease_ontology
DOID:11502
mitral valve insufficiency
A heart disease that is caused by high blood pressure.
ICD10CM:I11
ICD10CM:I11.9
ICD9CM:402
ICD9CM:402.9
SNOMEDCT_US_2016_03_01:155297007
SNOMEDCT_US_2016_03_01:194769003
SNOMEDCT_US_2016_03_01:194772005
SNOMEDCT_US_2016_03_01:64715009
UMLS_CUI:C0152105
disease_ontology
DOID:11516
hypertensive heart disease
ICD10CM:H35.03
ICD9CM:362.11
MESH:D058437
NCI:C3514
SNOMEDCT_US_2016_03_01:155108001
SNOMEDCT_US_2016_03_01:193356005
SNOMEDCT_US_2016_03_01:193358006
SNOMEDCT_US_2016_03_01:421731000
SNOMEDCT_US_2016_03_01:422001004
SNOMEDCT_US_2016_03_01:6962006
UMLS_CUI:C0152132
disease_ontology
DOID:11561
hypertensive retinopathy
ICD10CM:I12
ICD10CM:N26.9
ICD9CM:587
MESH:D009400
SNOMEDCT_US_2016_03_01:194773000
SNOMEDCT_US_2016_03_01:197658002
SNOMEDCT_US_2016_03_01:197662008
SNOMEDCT_US_2016_03_01:32916005
UMLS_CUI:C0027719
renal sclerosis
disease_ontology
DOID:11664
nephrosclerosis
DOID:3147
ICD10CM:E78.5
MESH:D006949
MESH:D006951
NCI:C34707
NCI:C34709
SNOMEDCT_US_2016_03_01:154739000
SNOMEDCT_US_2016_03_01:154743001
SNOMEDCT_US_2016_03_01:190782002
SNOMEDCT_US_2016_03_01:267499005
SNOMEDCT_US_2016_03_01:3744001
SNOMEDCT_US_2016_03_01:55822004
UMLS_CUI:C0020473
UMLS_CUI:C0020476
familial hyperlipoproteinemia
hyperlipemia
disease_ontology
hyperlipidaemia
DOID:1168
familial hyperlipidemia
A nervous system cancer that is located_in the peripheral nervous system.
DOID:3194
MESH:D010524
MESH:D018317
NCI:C3321
NCI:C4972
SNOMEDCT_US_2016_03_01:115242003
SNOMEDCT_US_2016_03_01:126980002
SNOMEDCT_US_2016_03_01:134214003
SNOMEDCT_US_2016_03_01:189946005
SNOMEDCT_US_2016_03_01:189953001
UMLS_CUI:C0031118
UMLS_CUI:C0206727
neoplasm of peripheral nerve (disorder)
nerve sheath neoplasm
nerve sheath tumors
tumor of PNS
disease_ontology
DOID:1192
peripheral nervous system neoplasm
A placenta disease that is characterized by a deficiency of amniotic fluid sometimes resulting in an embryonic defect through adherence between embryo and amnion.
DOID:12595
DOID:12596
ICD10CM:O41.0
ICD10CM:O41.00
ICD9CM:658.0
MESH:D016104
NCI:C92839
SNOMEDCT_US_2016_03_01:156190009
SNOMEDCT_US_2016_03_01:157051001
SNOMEDCT_US_2016_03_01:199652007
SNOMEDCT_US_2016_03_01:199656005
SNOMEDCT_US_2016_03_01:59566000
UMLS_CUI:C0079924
Oligohydramnios - delivered
antepartum oligohydramnios
delivered oligohydramnios
disease_ontology
DOID:12215
oligohydramnios
A pneumonia involving inflammation of lungs that begins in the terminal bronchioles, which become clogged with thick mucus that forms consolidated patches in adjacent lobules. It is caused by bacteria and viruses.
ICD10CM:J18.0
ICD9CM:485
MESH:D001996
NCI:C26710
SNOMEDCT_US_2016_03_01:155551009
SNOMEDCT_US_2016_03_01:195914001
SNOMEDCT_US_2016_03_01:266352008
SNOMEDCT_US_2016_03_01:396285007
SNOMEDCT_US_2016_03_01:67814005
UMLS_CUI:C0006285
Chest infection - unspecified bronchopneumonia
bronchial pneumonia
lobular pneumonia
disease_ontology
DOID:12375
bronchopneumonia
DOID:13997
DOID:9474
ICD10CM:D68.9
ICD9CM:286
MESH:D001778
NCI:C2902
SNOMEDCT_US_2016_03_01:127073005
SNOMEDCT_US_2016_03_01:154815003
SNOMEDCT_US_2016_03_01:191303002
SNOMEDCT_US_2016_03_01:267562007
SNOMEDCT_US_2016_03_01:362970003
SNOMEDCT_US_2016_03_01:64779008
UMLS_CUI:C0005779
postpartum coagulation defect
postpartum coagulation defect with delivery
disease_ontology
DOID:1247
blood coagulation disease
ICD10CM:H35.82
ICD9CM:362.84
SNOMEDCT_US_2016_03_01:193427006
SNOMEDCT_US_2016_03_01:26468004
UMLS_CUI:C0162291
disease_ontology
DOID:12510
retinal ischemia
A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis.
DOID:73
ICD9CM:429.2
MESH:D002318
NCI:C2931
SNOMEDCT_US_2016_03_01:155263000
SNOMEDCT_US_2016_03_01:194707003
SNOMEDCT_US_2016_03_01:195139006
SNOMEDCT_US_2016_03_01:195594006
SNOMEDCT_US_2016_03_01:266275004
SNOMEDCT_US_2016_03_01:266336005
SNOMEDCT_US_2016_03_01:49601007
UMLS_CUI:C0007222
disease of subdivision of hemolymphoid system
disease_ontology
DOID:1287
cardiovascular system disease
An intrinsic cardiomyopathy that is characterized by an an enlarged heart and damage to the myocardium causing the heart to pump blood inefficiently.
EFO:0000407
ICD10CM:I42.0
KEGG:05414
MESH:D002311
NCI:C84673
OMIM:PS115200
ORDO:217604
SNOMEDCT_US_2016_03_01:195018001
SNOMEDCT_US_2016_03_01:195021004
SNOMEDCT_US_2016_03_01:389995008
SNOMEDCT_US_2016_03_01:399020009
SNOMEDCT_US_2016_03_01:74368002
UMLS_CUI:C0007193
primary dilated cardiomyopathy
disease_ontology
Congestive cardiomyopathy
Familial dilated cardiomyopathy
Idiopathic dilation cardiomyopathy
DOID:12930
Xref MGI.
OMIM mapping confirmed by DO. [LS].
dilated cardiomyopathy
ICD10CM:H34.23
ICD9CM:362.32
MESH:D015356
NCI:C34436
SNOMEDCT_US_2016_03_01:50821009
UMLS_CUI:C0006123
Arterial retinal branch occlusion (disorder)
Retinal Arterial Branch Occlusion
Retinal arterial branch occlusion
disease_ontology
DOID:13094
branch retinal artery occlusion
DOID:3945
EFO:0004236
MESH:D005923
NCI:C37308
OMIM:PS603278
SNOMEDCT_US_2016_03_01:236403004
SNOMEDCT_US_2016_03_01:25821008
UMLS_CUI:C0017668
FGS (focal glomerular sclerosis)
FSGS
focal glomerular sclerosis
focal glomerulosclerosis
disease_ontology
DOID:1312
Xref MGI.
OMIM mapping confirmed by DO. [SN].
focal segmental glomerulosclerosis
A cystitis characterized by a sudden onset or severe symptoms.
ICD10CM:N30.0
ICD9CM:595.0
NCI:C26934
SNOMEDCT_US_2016_03_01:155883005
SNOMEDCT_US_2016_03_01:197833009
SNOMEDCT_US_2016_03_01:266628008
SNOMEDCT_US_2016_03_01:68226007
UMLS_CUI:C0149523
urinary tract infection
disease_ontology
DOID:13148
acute cystitis
A uterine benign neoplasm derived from the smooth muscle layer of the uterus.
EFO:0000731
ICD10CM:D25
ICD10CM:D25.9
ICD9CM:218
ICD9CM:218.9
MESH:D007889
NCI:C3434
OMIM:150699
SNOMEDCT_US_2016_03_01:146801000119103
SNOMEDCT_US_2016_03_01:154616000
SNOMEDCT_US_2016_03_01:189106003
SNOMEDCT_US_2016_03_01:44598004
SNOMEDCT_US_2016_03_01:95315005
UMLS_CUI:C0042133
Plexiform leiomyoma
UTERUS FIBROMA
leiomyoma of Corpus Uteri
uterine leiomyoma
disease_ontology
DOID:13223
OMIM mapping confirmed by DO. [LS].
uterine fibroid
A respiratory system cancer that is located_in the lung.
DOID:13075
DOID:1322
DOID:9881
ICD10CM:C34.1
ICD10CM:C34.2
ICD10CM:C34.3
ICD9CM:162.3
ICD9CM:162.4
ICD9CM:162.5
ICD9CM:162.8
OMIM:211980
OMIM:608935
OMIM:612571
OMIM:612593
OMIM:614210
SNOMEDCT_US_2016_03_01:187860004
SNOMEDCT_US_2016_03_01:187863002
SNOMEDCT_US_2016_03_01:187864008
SNOMEDCT_US_2016_03_01:187867001
SNOMEDCT_US_2016_03_01:187868006
SNOMEDCT_US_2016_03_01:187871003
SNOMEDCT_US_2016_03_01:187874006
SNOMEDCT_US_2016_03_01:269464000
UMLS_CUI:C0024624
UMLS_CUI:C0153491
UMLS_CUI:C0153492
UMLS_CUI:C0153493
disease_ontology
lung neoplasm
DOID:1324
lung cancer
ICD10CM:G91.1
ICD9CM:331.4
MESH:D006849
NCI:C116347
SNOMEDCT_US_2016_03_01:230746009
SNOMEDCT_US_2016_03_01:82346000
UMLS_CUI:C0549423
disease_ontology
DOID:14159
obstructive hydrocephalus
ICD9CM:331.9
SNOMEDCT_US_2016_03_01:154994001
SNOMEDCT_US_2016_03_01:154998003
SNOMEDCT_US_2016_03_01:192824002
SNOMEDCT_US_2016_03_01:267579001
SNOMEDCT_US_2016_03_01:267686002
SNOMEDCT_US_2016_03_01:267688001
SNOMEDCT_US_2016_03_01:418143002
SNOMEDCT_US_2016_03_01:52522001
SNOMEDCT_US_2016_03_01:73768007
UMLS_CUI:C0154671
Brain degeneration
disease_ontology
DOID:1443
cerebral degeneration
A disease that is characterized by abnormally rapid cell division.
DOID:0000818
cell process disease
neoplasm
disease_ontology
DOID:14566
disease of cellular proliferation
A sensory system disease that is located_in the eye or the adnexa of the eye.
ICD10CM:H35.00
ICD9CM:362.10
SNOMEDCT_US_2016_03_01:193355009
SNOMEDCT_US_2016_03_01:31411005
SNOMEDCT_US_2016_03_01:42873008
UMLS_CUI:C0004608
disease_ontology
DOID:1492
eye and adnexa disease
A disease of anatomical entity that is located_in reproductive system organs.
DOID:6309
NCI:C27613
UMLS_CUI:C1335037
genital system disease
disease_ontology
DOID:15
reproductive system disease
A disease that involves a psychological or behavioral pattern generally associated with subjective distress or disability that occurs in an individual, and which are not a part of normal development or culture.
ICD10CM:F99
ICD10CM:F99-F99
MESH:D001523
NCI:C2893
SNOMEDCT_US_2016_03_01:154843007
SNOMEDCT_US_2016_03_01:154971002
SNOMEDCT_US_2016_03_01:154972009
SNOMEDCT_US_2016_03_01:154980002
SNOMEDCT_US_2016_03_01:192637001
SNOMEDCT_US_2016_03_01:192639003
SNOMEDCT_US_2016_03_01:74732009
UMLS_CUI:C0004936
disease_ontology
DOID:150
disease of mental health
A thoracic disease which may involve inflammation of pleura, collection of air within the pleural cavity, abnormal collection of pleural fluid, abnormal growths on the pleura (pleural tumor) and pleural plaques. The main causes of pleural diseases including pleural effusions are congestive heart failure, malignancy, parapneumonic infections and pulmonary embolism.
DOID:1531
MESH:D010995
NCI:C26859
SNOMEDCT_US_2016_03_01:88075009
UMLS_CUI:C0032226
disorder of pleura
non-neoplastic pleural disease
disease_ontology
DOID:1532
pleural disease
A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm.
DOID:3226
ICD10CM:J96-J99
ICD10CM:J98
ICD9CM:510-519.99
ICD9CM:519
SNOMEDCT_US_2016_03_01:155603009
SNOMEDCT_US_2016_03_01:196057004
SNOMEDCT_US_2016_03_01:196184000
SNOMEDCT_US_2016_03_01:196255004
SNOMEDCT_US_2016_03_01:266373008
UMLS_CUI:C0029582
disease_ontology
DOID:1579
respiratory system disease
A blood platelet disease characterized by low a platelet count in the blood.
ICD10CM:D69.6
ICD9CM:287.5
MESH:D013921
NCI:C3408
OMIM:188000
OMIM:273900
OMIM:300367
OMIM:313900
OMIM:612004
ORDO:852
SNOMEDCT_US_2016_03_01:142969008
SNOMEDCT_US_2016_03_01:154827000
SNOMEDCT_US_2016_03_01:165556002
SNOMEDCT_US_2016_03_01:191326009
SNOMEDCT_US_2016_03_01:302215000
SNOMEDCT_US_2016_03_01:415116008
SNOMEDCT_US_2016_03_01:70786006
UMLS_CUI:C0040034
disease_ontology
DOID:1588
Xref MGI.
thrombocytopenia
ICD10CM:I15.0
MESH:D006978
NCI:C85044
SNOMEDCT_US_2016_03_01:123799005
SNOMEDCT_US_2016_03_01:194790006
UMLS_CUI:C0020545
Renovascular hypertension (disorder)
disease_ontology
DOID:1591
renovascular hypertension
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
ICD10CM:C80
ICD10CM:C80.1
ICD9CM:199
MESH:D009369
NCI:C9305
SNOMEDCT_US_2016_03_01:154432008
SNOMEDCT_US_2016_03_01:154433003
SNOMEDCT_US_2016_03_01:154577008
SNOMEDCT_US_2016_03_01:187597000
SNOMEDCT_US_2016_03_01:188475001
SNOMEDCT_US_2016_03_01:188482002
SNOMEDCT_US_2016_03_01:190150006
SNOMEDCT_US_2016_03_01:269513004
SNOMEDCT_US_2016_03_01:269623003
SNOMEDCT_US_2016_03_01:269626006
SNOMEDCT_US_2016_03_01:269634000
SNOMEDCT_US_2016_03_01:363346000
SNOMEDCT_US_2016_03_01:38807002
UMLS_CUI:C0006826
malignant neoplasm
malignant tumor
primary cancer
disease_ontology
DOID:162
Updating out dated UMLS CUI.
cancer
ICD10CM:J93.1
SNOMEDCT_US_2016_03_01:196103008
SNOMEDCT_US_2016_03_01:196105001
SNOMEDCT_US_2016_03_01:196251008
SNOMEDCT_US_2016_03_01:266367007
UMLS_CUI:C0029850
disease_ontology
DOID:1673
pneumothorax
ICD10CM:N30
ICD10CM:N30.9
ICD9CM:595
ICD9CM:595.9
MESH:D003556
NCI:C26738
SNOMEDCT_US_2016_03_01:155882000
SNOMEDCT_US_2016_03_01:155885003
SNOMEDCT_US_2016_03_01:197857009
SNOMEDCT_US_2016_03_01:266629000
SNOMEDCT_US_2016_03_01:38822007
UMLS_CUI:C0010692
disease_ontology
DOID:1679
cystitis
ICD10CM:H34
ICD10CM:H34.9
ICD9CM:362.3
ICD9CM:362.30
NCI:C34980
SNOMEDCT_US_2016_03_01:155111000
SNOMEDCT_US_2016_03_01:193373007
SNOMEDCT_US_2016_03_01:193380009
SNOMEDCT_US_2016_03_01:267717005
SNOMEDCT_US_2016_03_01:73757007
UMLS_CUI:C0035326
Retinal vasc. occlusion
Retinal vascular Occlusion
Retinal vascular occlusion (disorder)
Retinal vascular occlusion NOS (disorder)
Retinal vascular occlusion, unspecified
Unspecified retinal vascular occlusion (disorder)
disease_ontology
DOID:1729
retinal vascular occlusion
A cardiovascular system disease that primarily affects the blood vessels which includes the arteries, veins and capillaries that carry blood to and from the heart.
DOID:0000405
DOID:2403
DOID:2869
DOID:324
DOID:325
DOID:45
ICD10CM:I72.9
ICD9CM:442.9
MESH:D000783
MESH:D014652
MESH:D020758
MESH:D020760
NCI:C26693
NCI:C35117
SNOMEDCT_US_2016_03_01:134342004
SNOMEDCT_US_2016_03_01:155425005
SNOMEDCT_US_2016_03_01:155428007
SNOMEDCT_US_2016_03_01:195292009
SNOMEDCT_US_2016_03_01:27550009
SNOMEDCT_US_2016_03_01:362727005
SNOMEDCT_US_2016_03_01:371029002
SNOMEDCT_US_2016_03_01:432119003
SNOMEDCT_US_2016_03_01:85659009
UMLS_CUI:C0002940
UMLS_CUI:C0042373
UMLS_CUI:C0752127
UMLS_CUI:C0752130
vascular tissue disease
disease_ontology
DOID:178
vascular disease
A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra.
DOID:579
NCI:C27599
UMLS_CUI:C1335051
Non-neoplastic urinary tract disease
urinary tract disease
disease_ontology
DOID:18
urinary system disease
EFO:0004234
Sexual impotence (finding)
erectile dysfunction
disease_ontology
DOID:1875
impotence
ICD10CM:F52.9
ICD10CM:R37
MESH:D012735
NCI:C3347
SNOMEDCT_US_2016_03_01:225723003
SNOMEDCT_US_2016_03_01:231532002
SNOMEDCT_US_2016_03_01:39894007
SNOMEDCT_US_2016_03_01:56925008
SNOMEDCT_US_2016_03_01:65655009
UMLS_CUI:C0549622
disease_ontology
DOID:1876
sexual dysfunction
An acquired metabolic disease that has_material_basis_in an abnormally high level of uric acid in the blood.
MESH:D033461
NCI:C3961
SNOMEDCT_US_2016_03_01:144021008
SNOMEDCT_US_2016_03_01:166733000
SNOMEDCT_US_2016_03_01:237857006
SNOMEDCT_US_2016_03_01:271198001
SNOMEDCT_US_2016_03_01:35885006
UMLS_CUI:C0740394
(Blood urate raized) or (hyperuricemia)
uricacidemia
disease_ontology
DOID:1920
hyperuricemia
EFO:0003914
ICD10CM:I25.1
ICD10CM:I70
ICD9CM:440
MESH:D050197
NCI:C35768
NCI:C35771
SNOMEDCT_US_2016_03_01:155382007
SNOMEDCT_US_2016_03_01:155414001
SNOMEDCT_US_2016_03_01:194848007
SNOMEDCT_US_2016_03_01:195251000
SNOMEDCT_US_2016_03_01:266318005
SNOMEDCT_US_2016_03_01:38716007
UMLS_CUI:C0004153
disease_ontology
DOID:1936
atherosclerosis
ICD10CM:D69.9
ICD9CM:287.9
MESH:D006474
SNOMEDCT_US_2016_03_01:191327000
SNOMEDCT_US_2016_03_01:191331006
SNOMEDCT_US_2016_03_01:191437009
SNOMEDCT_US_2016_03_01:268884000
UMLS_CUI:C0019087
Hemorrhagic diathesis
Hemorrhagic disease
disease_ontology
DOID:2213
hemorrhagic disease
MESH:D001791
SNOMEDCT_US_2016_03_01:22716005
UMLS_CUI:C0005818
Thrombocytopathy
platelet disorder
disease_ontology
DOID:2218
blood platelet disease
DOID:2315
ICD10CM:G45.9
ICD9CM:435.8
MESH:D002546
NCI:C50781
SNOMEDCT_US_2016_03_01:155404005
SNOMEDCT_US_2016_03_01:195196001
SNOMEDCT_US_2016_03_01:195207009
SNOMEDCT_US_2016_03_01:266257000
SNOMEDCT_US_2016_03_01:266314007
SNOMEDCT_US_2016_03_01:313242003
SNOMEDCT_US_2016_03_01:38609002
UMLS_CUI:C0007787
UMLS_CUI:C0155728
TIA
TIA - Transient ischaemic attack
TRANSIENT ISCHEMIC ATTACK
Transient cerebral ischaemia
Transient cerebral ischaemia NOS
Transient cerebral ischemia (disorder) [Ambiguous]
Transient ischemic attacks (disorder)
transient ischemic attack
disease_ontology
DOID:224
transient cerebral ischemia
A reproductive system disease that impairs the ability to reproduce and is located in the uterus, vagina, cervix, ovaries or fallopian tubes.
ICD9CM:629.9
MESH:D005831
SNOMEDCT_US_2016_03_01:156032001
SNOMEDCT_US_2016_03_01:156066005
SNOMEDCT_US_2016_03_01:198486002
SNOMEDCT_US_2016_03_01:244938009
SNOMEDCT_US_2016_03_01:266680004
SNOMEDCT_US_2016_03_01:310789003
SNOMEDCT_US_2016_03_01:38233001
UMLS_CUI:C0017411
disease_ontology
DOID:229
female reproductive system disease
MESH:D002545
SNOMEDCT_US_2016_03_01:11890005
SNOMEDCT_US_2016_03_01:193049009
SNOMEDCT_US_2016_03_01:389100007
UMLS_CUI:C0007786
Ischaemic encephalopathy
Ischemic encephalopathy (disorder)
disease_ontology
DOID:2316
brain ischemia
ICD10CM:I25.1
ICD10CM:I70
ICD9CM:440
MESH:D050197
NCI:C34403
NCI:C35768
NCI:C35771
SNOMEDCT_US_2016_03_01:155382007
SNOMEDCT_US_2016_03_01:155414001
SNOMEDCT_US_2016_03_01:194848007
SNOMEDCT_US_2016_03_01:195121002
SNOMEDCT_US_2016_03_01:195251000
SNOMEDCT_US_2016_03_01:266318005
SNOMEDCT_US_2016_03_01:38716007
SNOMEDCT_US_2016_03_01:39468009
UMLS_CUI:C0004153
UMLS_CUI:C3665365
Arteriosclerotic Cardiovascular disease
Arteriosclerotic cardiovascular disease
Arteriosclerotic cardiovascular disease, NOS
Atherosclerotic Cardiovascular disease
Atherosclerotic cardiovascular disease
Cardiovascular arteriosclerosis unspecified (disorder)
disease_ontology
DOID:2348
arteriosclerotic cardiovascular disease
An artery disease that is characterized by a thickening and hardening of arterial walls in the arteries.
CSP:0571-2299
ICD10CM:I70
MESH:D001161
NCI:C34398
SNOMEDCT_US_2016_03_01:107671003
SNOMEDCT_US_2016_03_01:155414001
SNOMEDCT_US_2016_03_01:155418003
SNOMEDCT_US_2016_03_01:195251000
SNOMEDCT_US_2016_03_01:195257001
SNOMEDCT_US_2016_03_01:266318005
SNOMEDCT_US_2016_03_01:28960008
SNOMEDCT_US_2016_03_01:72092001
UMLS_CUI:C0003850
Arteriosclerosis (morphologic abnormality)
Arteriosclerosis NOS
Arteriosclerotic vascular disease (disorder)
Arteriosclerotic vascular disease NOS
disease_ontology
DOID:2349
arteriosclerosis
A hematopoietic system disease that is characterized by a decrease in the normal number of red blood cells.
EFO:0004272
ICD10CM:D64.9
ICD9CM:285.9
MESH:D000740
NCI:C2869
SNOMEDCT_US_2016_03_01:154786001
SNOMEDCT_US_2016_03_01:154812000
SNOMEDCT_US_2016_03_01:191277004
SNOMEDCT_US_2016_03_01:267531008
SNOMEDCT_US_2016_03_01:271737000
SNOMEDCT_US_2016_03_01:64593003
UMLS_CUI:C0002871
anaemia
disease_ontology
DOID:2355
PRISM.
anemia
ICD9CM:593.81
NCI:C35338
SNOMEDCT_US_2016_03_01:16934004
SNOMEDCT_US_2016_03_01:197814004
SNOMEDCT_US_2016_03_01:266559003
UMLS_CUI:C0268790
renal vascular disease
vascular disorder of kidney
disease_ontology
DOID:2388
renal artery disease
ICD10CM:D68.59
MESH:D018455
NCI:C99026
SNOMEDCT_US_2016_03_01:1563006
UMLS_CUI:C0242666
Protein S deficiency
Protein S deficiency disease (disorder)
disease_ontology
DOID:2451
protein S deficiency
ICD10CM:D68.59
MESH:D019851
NCI:C84479
OMIM:188050
OMIM:614486
SNOMEDCT_US_2016_03_01:191302007
SNOMEDCT_US_2016_03_01:234467004
SNOMEDCT_US_2016_03_01:76612001
UMLS_CUI:C0398623
hypercoagulability state
disease_ontology
DOID:2452
OMIM mapping confirmed by DO. [LS].
thrombophilia
MESH:D009401
SNOMEDCT_US_2016_03_01:90708001
UMLS_CUI:C0027720
disease_ontology
DOID:2527
nephrosis
An inherited metabolic disorder that involves elevated levels of bilirubin resulting from disruption of bilirubin metabolism.
DOID:2740
MESH:D006932
MESH:D006933
NCI:C84761
SNOMEDCT_US_2016_03_01:143932000
SNOMEDCT_US_2016_03_01:14783006
SNOMEDCT_US_2016_03_01:154770008
SNOMEDCT_US_2016_03_01:166612004
SNOMEDCT_US_2016_03_01:20505009
SNOMEDCT_US_2016_03_01:235904007
SNOMEDCT_US_2016_03_01:267509000
UMLS_CUI:C0020433
UMLS_CUI:C0020435
hereditary hyperbilirubinemia
hyperbilirubinemia
disease_ontology
hyperbilirubinaemia
DOID:2741
bilirubin metabolic disorder
ICD10CM:N12
MESH:D011702
NCI:C34964
SNOMEDCT_US_2016_03_01:197780007
SNOMEDCT_US_2016_03_01:27174002
UMLS_CUI:C0034183
disease_ontology
DOID:2744
pyelitis
MESH:D002526
SNOMEDCT_US_2016_03_01:155010002
SNOMEDCT_US_2016_03_01:192867005
SNOMEDCT_US_2016_03_01:223176004
SNOMEDCT_US_2016_03_01:224186005
SNOMEDCT_US_2016_03_01:267691001
SNOMEDCT_US_2016_03_01:307361005
SNOMEDCT_US_2016_03_01:49784007
UMLS_CUI:C0007760
disease_ontology
DOID:2786
cerebellar disease
A nephritis that causes inflammation of the glomeruli located_in kidney.
ICD10CM:N05
ICD10CM:N08
MESH:D005921
NCI:C26784
SNOMEDCT_US_2016_03_01:197648001
SNOMEDCT_US_2016_03_01:36171008
UMLS_CUI:C0017658
disease_ontology
DOID:2921
glomerulonephritis
MESH:D001002
NCI:C114699
SNOMEDCT_US_2016_03_01:139460001
SNOMEDCT_US_2016_03_01:158479000
SNOMEDCT_US_2016_03_01:207182009
SNOMEDCT_US_2016_03_01:2472002
UMLS_CUI:C0003460
Suppression of urinary secretion
disease_ontology
DOID:2983
anuria
A glomerulonephritis characterized by build up of IgA antibody in the glomerulus.
EFO:0004194
MESH:D005922
NCI:C34643
NCI:C35280
OMIM:161950
SNOMEDCT_US_2016_03_01:236407003
SNOMEDCT_US_2016_03_01:68779003
UMLS_CUI:C0017661
Berger's IgA or IgG nephropathy
Focal Glomerulonephritis
IGA glomerulonephritis
IgA nephropathy
primary IgA nephropathy
segmental glomerulonephritis
disease_ontology
DOID:2986
OMIM mapping confirmed by DO. [SN].
IgA glomerulonephritis
A substance-related disorder that involves a maladaptive pattern of substance use leading to significant impairment in functioning.
MESH:D019966
NCI:C16522
SNOMEDCT_US_2016_03_01:26416006
UMLS_CUI:C0013146
disease_ontology
DOID:302
substance abuse
disease_ontology
DOID:3021
acute kidney failure
A disease of mental health involving the abuse or dependence on a substance that is ingested in order to produce a high, alter one's senses, or otherwise affect functioning.
MESH:D019966
NCI:C92203
UMLS_CUI:C0236969
disease_ontology
DOID:303
substance-related disorder
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
DOID:2428
DOID:6570
CSP:2000-1867
MESH:D002277
MESH:D009375
NCI:C2916
NCI:C3709
SNOMEDCT_US_2016_03_01:118285006
SNOMEDCT_US_2016_03_01:134207000
SNOMEDCT_US_2016_03_01:154433003
SNOMEDCT_US_2016_03_01:188083002
SNOMEDCT_US_2016_03_01:189546004
SNOMEDCT_US_2016_03_01:189549006
SNOMEDCT_US_2016_03_01:189559007
SNOMEDCT_US_2016_03_01:269513004
SNOMEDCT_US_2016_03_01:68453008
SNOMEDCT_US_2016_03_01:71298006
UMLS_CUI:C0007097
UMLS_CUI:C0553707
UMLS_CUI:C1368683
epithelioma
malignant Epithelioma
disease_ontology
DOID:305
carcinoma
An organ system cancer located_in the nervous system that affects the central or peripheral nervous system.
DOID:1193
DOID:3195
DOID:4695
ICD9CM:192
ICD9CM:192.9
MESH:D009380
NCI:C35562
SNOMEDCT_US_2016_03_01:188306000
UMLS_CUI:C0027665
UMLS_CUI:C0153643
UMLS_CUI:C1334956
malignant neoplasm of nervous system
neoplasm of nervous system (disorder)
nervous system neoplasm
neural neoplasm
neural tumor
tumor of the nervous system
disease_ontology
DOID:3093
nervous system cancer
An organ system cancer located_in gastrointestinal tract that is manifested in organs of the gastrointestinal system.
DOID:4945
DOID:8377
ICD10CM:C26.9
ICD9CM:239.0
MESH:D004067
MESH:D005770
NCI:C3052
NCI:C4890
SNOMEDCT_US_2016_03_01:126768004
SNOMEDCT_US_2016_03_01:128348002
SNOMEDCT_US_2016_03_01:128415001
SNOMEDCT_US_2016_03_01:189527000
SNOMEDCT_US_2016_03_01:276806006
SNOMEDCT_US_2016_03_01:367543008
SNOMEDCT_US_2016_03_01:428905002
SNOMEDCT_US_2016_03_01:93811007
UMLS_CUI:C0012243
UMLS_CUI:C0017185
UMLS_CUI:C0685938
GI tumor
digestive system cancer
gastrointestinal tract cancer
disease_ontology
DOID:3119
gastrointestinal system cancer
An inherited metabolic disorder that involves the creation and degradation of lipids.
MESH:D008052
UMLS_CUI:C0023772
dyslipidemia
fatty acid metabolism disorder
disease_ontology
DOID:3146
lipid metabolism disorder
A peripheral nervous system neoplasm that is located_in the connective tissue surrounding nerves.
MESH:D018317
UMLS_CUI:C0751689
neoplasm of the nerve Sheath
nerve sheath tumour
disease_ontology
DOID:3193
peripheral nerve sheath neoplasm
A vascular disease that is characterized by a restriction in blood supply to tissues.
MESH:D007511
MESH:D054058
NCI:C34738
SNOMEDCT_US_2016_03_01:52674009
UMLS_CUI:C0022116
disease_ontology
DOID:326
ischemia
A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system.
ICD10CM:G96.9
MESH:D002493
NCI:C2934
SNOMEDCT_US_2016_03_01:138748005
SNOMEDCT_US_2016_03_01:154981003
SNOMEDCT_US_2016_03_01:155049004
SNOMEDCT_US_2016_03_01:155059003
SNOMEDCT_US_2016_03_01:192641002
SNOMEDCT_US_2016_03_01:193076009
SNOMEDCT_US_2016_03_01:194566008
SNOMEDCT_US_2016_03_01:23853001
SNOMEDCT_US_2016_03_01:267144009
SNOMEDCT_US_2016_03_01:267679005
SNOMEDCT_US_2016_03_01:267700003
SNOMEDCT_US_2016_03_01:267702006
SNOMEDCT_US_2016_03_01:275539005
UMLS_CUI:C0007682
disease_ontology
DOID:331
central nervous system disease
An artery disease that is characterized by plaque building up along the inner walls of the arteries of the heart resulting in a narrowing of the arteries and a reduced blood supply to the cardiac muscles.
DOID:10506
DOID:3363
DOID:3394
DOID:9420
EFO:0001645
ICD10CM:I20-I25
ICD10CM:I25
ICD10CM:I25.1
ICD10CM:I25.10
ICD10CM:I25.9
ICD10CM:K76.1
ICD9CM:410-414.99
ICD9CM:414.0
ICD9CM:414.9
MESH:D003324
MESH:D003327
MESH:D017202
NCI:C35505
NCI:C50625
OMIM:300464
OMIM:607339
OMIM:608316
OMIM:608318
OMIM:608320
OMIM:610947
OMIM:611139
OMIM:612030
OMIM:614293
SNOMEDCT_US_2016_03_01:155303000
SNOMEDCT_US_2016_03_01:155315001
SNOMEDCT_US_2016_03_01:155316000
SNOMEDCT_US_2016_03_01:155318004
SNOMEDCT_US_2016_03_01:155322009
SNOMEDCT_US_2016_03_01:194795001
SNOMEDCT_US_2016_03_01:194841001
SNOMEDCT_US_2016_03_01:194852007
SNOMEDCT_US_2016_03_01:194878003
SNOMEDCT_US_2016_03_01:195540001
SNOMEDCT_US_2016_03_01:233822007
SNOMEDCT_US_2016_03_01:2610009
SNOMEDCT_US_2016_03_01:266231003
SNOMEDCT_US_2016_03_01:266290000
SNOMEDCT_US_2016_03_01:266291001
SNOMEDCT_US_2016_03_01:271430002
SNOMEDCT_US_2016_03_01:32598000
SNOMEDCT_US_2016_03_01:413838009
SNOMEDCT_US_2016_03_01:413844008
SNOMEDCT_US_2016_03_01:414545008
SNOMEDCT_US_2016_03_01:414795007
SNOMEDCT_US_2016_03_01:41702007
SNOMEDCT_US_2016_03_01:443502000
SNOMEDCT_US_2016_03_01:53741008
SNOMEDCT_US_2016_03_01:84537008
UMLS_CUI:C0010054
UMLS_CUI:C0010068
UMLS_CUI:C0151744
UMLS_CUI:C0264694
CHD (coronary heart disease)
Coronary disease
coronary arteriosclerosis
coronary heart disease
disease_ontology
DOID:3393
Xref MGI.
coronary artery disease
A vascular disease that is characterized by obstruction of larger arteries not within the coronary, aortic arch vasculature, or brain.
DOID:2868
ICD9CM:443.81
MESH:D001157
MESH:D016481
SNOMEDCT_US_2016_03_01:195624006
SNOMEDCT_US_2016_03_01:2929001
UMLS_CUI:C0003838
UMLS_CUI:C0031115
arterial occlusive disease
disease_ontology
DOID:341
peripheral vascular disease
A female reproductive system disease that is located_in the uterus.
ICD10CM:N85.9
ICD9CM:621.9
MESH:D014591
NCI:C26907
SNOMEDCT_US_2016_03_01:12337004
SNOMEDCT_US_2016_03_01:156004005
SNOMEDCT_US_2016_03_01:156009000
SNOMEDCT_US_2016_03_01:198335006
SNOMEDCT_US_2016_03_01:237068005
UMLS_CUI:C0042131
disease_ontology
DOID:345
uterine disease
A urinary system disease that is located_in the bladder.
ICD10CM:N32.9
ICD9CM:596.9
MESH:D001745
NCI:C2900
SNOMEDCT_US_2016_03_01:155886002
SNOMEDCT_US_2016_03_01:155890000
SNOMEDCT_US_2016_03_01:197897007
SNOMEDCT_US_2016_03_01:266630005
SNOMEDCT_US_2016_03_01:42643001
UMLS_CUI:C0005686
Urinary Bladder Disease
disease_ontology
DOID:365
bladder disease
MESH:D003389
NCI:C26941
SNOMEDCT_US_2016_03_01:73013002
UMLS_CUI:C0151311
Cranial nerve Paralysis
Cranial nerve palsy
disease_ontology
DOID:3817
cranial nerve palsy
A lung cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells and is located_in the lungs and has_symptom cough and has_symptom chest discomfort or pain and has_symptom weight loss and has_symptom hemoptysis.
EFO:0001071
ICD10CM:C34.90
NCI:C4878
SNOMEDCT_US_2016_03_01:154485001
SNOMEDCT_US_2016_03_01:187875007
SNOMEDCT_US_2016_03_01:269561006
UMLS_CUI:C0684249
cancer of lung
disease_ontology
carcinoma of lung
DOID:3905
OMIM mapping confirmed by DO. [SN].
lung carcinoma
A lung carcinoma that is characterized as any type of epithelial lung cancer other than small cell lung carcinoma.
EFO:0003060
ICD10CM:C34
KEGG:05223
MESH:D002289
NCI:C2926
SNOMEDCT_US_2016_03_01:254637007
UMLS_CUI:C0007131
NSCLC
Non-small cell lung cancer
disease_ontology
DOID:3908
non-small cell lung carcinoma
A gastrointestinal system disease that is located_in the mouth.
MESH:D009059
NCI:C27641
NCI:C3240
SNOMEDCT_US_2016_03_01:118938008
SNOMEDCT_US_2016_03_01:155630004
SNOMEDCT_US_2016_03_01:266484002
UMLS_CUI:C0026636
disease_ontology
DOID:403
mouth disease
A heart disease involving one or more of the four valves of the heart (the aortic and mitral valves on the left and the pulmonary and tricuspid valves on the right).
DOID:989
MESH:D006349
MESH:D016127
NCI:C45525
SNOMEDCT_US_2016_03_01:195013005
SNOMEDCT_US_2016_03_01:368009
SNOMEDCT_US_2016_03_01:398995000
UMLS_CUI:C0018824
UMLS_CUI:C0079485
Valvular heart disease
disease_ontology
DOID:4079
heart valve disease
MESH:D044882
NCI:C53655
SNOMEDCT_US_2016_03_01:126877002
UMLS_CUI:C1257958
disorder of glucose metabolism (disorder)
disease_ontology
DOID:4194
glucose metabolism disease
A carcinoma that is composed of large, monotonous rounded or overtly polygonal-shaped cells with abundant cytoplasm.
MESH:D018287
NCI:C3780
SNOMEDCT_US_2016_03_01:189551005
SNOMEDCT_US_2016_03_01:22687000
UMLS_CUI:C0206704
disease_ontology
DOID:4552
large cell carcinoma
NCI:C4450
SNOMEDCT_US_2016_03_01:254629004
UMLS_CUI:C0345958
large cell carcinoma of lung (disorder)
large cell lung carcinoma
disease_ontology
DOID:4556
lung large cell carcinoma
An artery disease that is characterized by degeneration of the cells composing the aortic wall.
MESH:D001018
NCI:C101253
SNOMEDCT_US_2016_03_01:47040006
UMLS_CUI:C0003493
aortic disorder
disorder of the aorta (disorder)
disease_ontology
DOID:520
aortic disease
A lung disease that involves lung parenchyma or alveolar inflammation and abnormal alveolar filling with fluid (consolidation and exudation). It results from a variety of causes including infection with bacteria, viruses, fungi or parasites, and chemical or physical injury to the lungs. It is accompanied by fever, chills, cough, and difficulty in breathing.
DOID:10509
DOID:11742
DOID:5871
MESH:D011014
NCI:C3333
SNOMEDCT_US_2016_03_01:155548002
SNOMEDCT_US_2016_03_01:155552002
SNOMEDCT_US_2016_03_01:155558003
SNOMEDCT_US_2016_03_01:233604007
SNOMEDCT_US_2016_03_01:266391003
SNOMEDCT_US_2016_03_01:274103002
SNOMEDCT_US_2016_03_01:60363000
UMLS_CUI:C0032285
acute pneumonia
disease_ontology
DOID:552
pneumonia
A urinary system disease that is located_in the kidney.
EFO:0003086
ICD10CM:N08
ICD10CM:N28.9
MESH:D007674
NCI:C3149
NCI:C34843
SNOMEDCT_US_2016_03_01:155871008
SNOMEDCT_US_2016_03_01:266612003
SNOMEDCT_US_2016_03_01:266624005
SNOMEDCT_US_2016_03_01:266627003
SNOMEDCT_US_2016_03_01:274108006
SNOMEDCT_US_2016_03_01:90708001
UMLS_CUI:C0022658
nephropathy
disease_ontology
DOID:557
kidney disease
An eye and adnexa disease that is located_in the eye.
DOID:2933
ICD10CM:H44
ICD10CM:H44.9
ICD9CM:360
ICD9CM:360.9
ICD9CM:379.90
MESH:D005128
NCI:C26767
SNOMEDCT_US_2016_03_01:111509007
SNOMEDCT_US_2016_03_01:155101007
SNOMEDCT_US_2016_03_01:155198005
SNOMEDCT_US_2016_03_01:193265001
SNOMEDCT_US_2016_03_01:193266000
SNOMEDCT_US_2016_03_01:193316008
SNOMEDCT_US_2016_03_01:194183009
SNOMEDCT_US_2016_03_01:264555006
SNOMEDCT_US_2016_03_01:366261005
SNOMEDCT_US_2016_03_01:371405004
SNOMEDCT_US_2016_03_01:371409005
SNOMEDCT_US_2016_03_01:79517001
UMLS_CUI:C0015397
disease_ontology
DOID:5614
eye disease
A neuropathy that is located_in one of the twelve cranial nerves.
ICD10CM:G52.9
ICD9CM:352.9
MESH:D003389
NCI:C26733
SNOMEDCT_US_2016_03_01:193104009
SNOMEDCT_US_2016_03_01:267598004
SNOMEDCT_US_2016_03_01:267709002
SNOMEDCT_US_2016_03_01:276379008
SNOMEDCT_US_2016_03_01:73013002
UMLS_CUI:C0010266
Cranial nerve disorder
disorder of cranial nerve
disease_ontology
DOID:5656
cranial nerve disease
An eye disease that is located_in the retina.
ICD10CM:H35.9
ICD9CM:362.9
MESH:D012164
NCI:C26875
NCI:C62601
SNOMEDCT_US_2016_03_01:193430004
SNOMEDCT_US_2016_03_01:267715002
SNOMEDCT_US_2016_03_01:29555009
SNOMEDCT_US_2016_03_01:35426003
SNOMEDCT_US_2016_03_01:399625000
UMLS_CUI:C0035309
disease_ontology
DOID:5679
retinal disease
A nervous system disease that affects the peripheral nervous system.
DOID:13069
ICD10CM:G64
ICD9CM:350-359.99
MESH:D010523
NCI:C119734
NCI:C27580
NCI:C27587
SNOMEDCT_US_2016_03_01:155064004
SNOMEDCT_US_2016_03_01:155080009
SNOMEDCT_US_2016_03_01:155100008
SNOMEDCT_US_2016_03_01:193088006
SNOMEDCT_US_2016_03_01:193264002
SNOMEDCT_US_2016_03_01:264554005
SNOMEDCT_US_2016_03_01:267706009
SNOMEDCT_US_2016_03_01:302226006
SNOMEDCT_US_2016_03_01:42658009
UMLS_CUI:C0031117
UMLS_CUI:C1335029
disease_ontology
peripheral nerve disease
peripheral neuropathy
DOID:574
peripheral nervous system disease
ICD10CM:R80
ICD10CM:R80.9
ICD9CM:791.0
MESH:D011507
NCI:C38012
SNOMEDCT_US_2016_03_01:144515004
SNOMEDCT_US_2016_03_01:158565005
SNOMEDCT_US_2016_03_01:158568007
SNOMEDCT_US_2016_03_01:167279003
SNOMEDCT_US_2016_03_01:207310001
SNOMEDCT_US_2016_03_01:207315006
SNOMEDCT_US_2016_03_01:232691000
SNOMEDCT_US_2016_03_01:236719005
SNOMEDCT_US_2016_03_01:29738008
UMLS_CUI:C0033687
disease_ontology
DOID:576
proteinuria
ICD10CM:D55-D59
MESH:D000743
NCI:C34376
OMIM:266120
OMIM:612631
SNOMEDCT_US_2016_03_01:191231008
SNOMEDCT_US_2016_03_01:191416001
SNOMEDCT_US_2016_03_01:61261009
UMLS_CUI:C0002878
ANEMIA HEMOLYTIC
disease_ontology
DOID:583
OMIM mapping confirmed by DO. [SN].
OMIM mapping by NeuroDevNet. [LS].
hemolytic anemia
A coronary artery disease characterized by myocardial cell death (myocardial necrosis) due to prolonged ischaemia.
EFO:0000612
ICD10CM:I21
ICD10CM:I22
MESH:D009203
NCI:C27996
OMIM:608557
SNOMEDCT_US_2016_03_01:155304006
SNOMEDCT_US_2016_03_01:194796000
SNOMEDCT_US_2016_03_01:22298006
SNOMEDCT_US_2016_03_01:233824008
SNOMEDCT_US_2016_03_01:266288001
SNOMEDCT_US_2016_03_01:66514008
UMLS_CUI:C0027051
Myocardial infarct
heart attack
disease_ontology
DOID:5844
Xref MGI.
myocardial infarction
A heart disease that is characterized by any structural or functional cardiac disorder that impairs the ability of the heart to fill with or pump a sufficient amount of blood throughout the body.
DOID:395
ICD10CM:I50
ICD10CM:I50.9
ICD9CM:428
ICD9CM:428.0
ICD9CM:428.9
MESH:D006333
NCI:C3080
NCI:C50577
SNOMEDCT_US_2016_03_01:155374007
SNOMEDCT_US_2016_03_01:155375008
SNOMEDCT_US_2016_03_01:155377000
SNOMEDCT_US_2016_03_01:195108009
SNOMEDCT_US_2016_03_01:195117009
SNOMEDCT_US_2016_03_01:266248006
SNOMEDCT_US_2016_03_01:266308000
SNOMEDCT_US_2016_03_01:42343007
SNOMEDCT_US_2016_03_01:84114007
UMLS_CUI:C0018801
UMLS_CUI:C0018802
CHF
Cardiac Failure Congestive
Congestive heart disease
Weak heart
disease_ontology
DOID:6000
congestive heart failure
DOID:11505
DOID:58
DOID:59
ICD10CM:I05
ICD10CM:I05.1
ICD10CM:I05.9
ICD9CM:394
ICD9CM:394.1
ICD9CM:424.0
NCI:C78446
SNOMEDCT_US_2016_03_01:11851006
SNOMEDCT_US_2016_03_01:155276006
SNOMEDCT_US_2016_03_01:155278007
SNOMEDCT_US_2016_03_01:155279004
SNOMEDCT_US_2016_03_01:194724009
SNOMEDCT_US_2016_03_01:194729004
SNOMEDCT_US_2016_03_01:194982000
SNOMEDCT_US_2016_03_01:250998008
SNOMEDCT_US_2016_03_01:266278002
SNOMEDCT_US_2016_03_01:266279005
SNOMEDCT_US_2016_03_01:31085000
SNOMEDCT_US_2016_03_01:83898004
UMLS_CUI:C0026265
UMLS_CUI:C0155563
UMLS_CUI:C0264765
Mitral RH valve dis.
Rheumatic disease of mitral valve (disorder)
Rheumatic mitral insufficiency
Rheumatic mitral valve changes
Rheumatic mitral valve regurgitation
chronic rheumatic mitral valve (disorder)
disease of mitral valve
rheumatic disease of mitral valve
rheumatic mitral valve incompetence
disease_ontology
DOID:61
mitral valve disease
MESH:D001796
UMLS_CUI:C0005830
blood protein disorder
disease_ontology
DOID:620
blood protein disease
A disease that has_material_basis_in genetic variations in the human genome.
MESH:D030342
NCI:C3101
SNOMEDCT_US_2016_03_01:264530000
SNOMEDCT_US_2016_03_01:32895009
UMLS_CUI:C0019247
disease_ontology
DOID:630
genetic disease
A disease of metabolism that is characterized by enzyme deficiency or accumulation of enzymes or toxins which interfere with normal function due to inherited enzyme abnormality.
MESH:D008661
NCI:C34816
SNOMEDCT_US_2016_03_01:363205007
SNOMEDCT_US_2016_03_01:86095007
UMLS_CUI:C0025521
Inborn Errors of Metabolism
Metabolic hereditary disorder
inborn metabolism disorder
disease_ontology
DOID:655
inherited metabolic disorder
An artery disease that is characterized by dysfunction of the blood vessels supplying the brain.
DOID:12214
DOID:3455
DOID:8231
EFO:0000712
ICD10CM:I60-I69
ICD10CM:I63.9
ICD10CM:I67.9
ICD9CM:430-438.99
ICD9CM:437.9
MESH:D002561
MESH:D020521
NCI:C2938
NCI:C3390
OMIM:601367
SNOMEDCT_US_2016_03_01:155388006
SNOMEDCT_US_2016_03_01:155405006
SNOMEDCT_US_2016_03_01:155412002
SNOMEDCT_US_2016_03_01:195208004
SNOMEDCT_US_2016_03_01:195249004
SNOMEDCT_US_2016_03_01:195595007
SNOMEDCT_US_2016_03_01:230690007
SNOMEDCT_US_2016_03_01:266312006
SNOMEDCT_US_2016_03_01:266315008
SNOMEDCT_US_2016_03_01:270883006
SNOMEDCT_US_2016_03_01:313267000
SNOMEDCT_US_2016_03_01:62914000
SNOMEDCT_US_2016_03_01:82797006
UMLS_CUI:C0007820
UMLS_CUI:C0038454
CVA (cerebral vascular accident)
Cerebrovascular accident (disorder)
cerebrovascular accident
cerebrovascular disorder
stroke
disease_ontology
DOID:6713
OMIM mapping confirmed by DO. [SN].
cerebrovascular disease
ICD10CM:H35.81
ICD9CM:362.83
MESH:D010211
SNOMEDCT_US_2016_03_01:193426002
SNOMEDCT_US_2016_03_01:6141006
UMLS_CUI:C0242420
disease_ontology
DOID:6929
retinal edema
A disease that manifests in a defined anatomical structure.
DOID:1
DOID:2
DOID:5
DOID:71
DOID:72
DOID:8
disease_ontology
DOID:7
disease of anatomical entity
NCI:C35142
SNOMEDCT_US_2016_03_01:300980002
UMLS_CUI:C0085577
ANEMIA NORMOCYTIC
Normocytic anemia (disorder)
disease_ontology
DOID:720
normocytic anemia
An immune system disease that has_material_basis_in hematopoietic cells.
ICD10CM:D75.9
ICD9CM:280-289.99
ICD9CM:289.9
MESH:D006402
NCI:C26323
SNOMEDCT_US_2016_03_01:154785002
SNOMEDCT_US_2016_03_01:154842002
SNOMEDCT_US_2016_03_01:191124002
SNOMEDCT_US_2016_03_01:191402006
SNOMEDCT_US_2016_03_01:191446003
SNOMEDCT_US_2016_03_01:267552000
SNOMEDCT_US_2016_03_01:267573000
SNOMEDCT_US_2016_03_01:34093004
UMLS_CUI:C0018939
Blood disease
Blood dyscrasia NOS
DISEASE OF THE BLOOD AND BLOOD-FORMING ORGANS
Hematological disease
blood disorder
disease of hematopoietic system
disease_ontology
DOID:74
hematopoietic system disease
A disease of anatomical entity that is located_in the gastrointestinal tract.
DOID:27
DOID:944
ICD10CM:K92.9
ICD9CM:520-579.99
MESH:D004066
SNOMEDCT_US_2016_03_01:155629009
SNOMEDCT_US_2016_03_01:155847001
SNOMEDCT_US_2016_03_01:197575000
SNOMEDCT_US_2016_03_01:266483008
SNOMEDCT_US_2016_03_01:53619000
UMLS_CUI:C0012242
GIT disease
Gastroenteropathy
alimentary system disease
digestive system disorder
gastrointestinal disease
gastrointestinal disorder
disease_ontology
DOID:77
gastrointestinal system disease
A uterine disease that is located_in the placenta.
DOID:1815
DOID:5366
DOID:9219
ICD10CM:O43
ICD10CM:O43.9
ICD10CM:O43.90
ICD9CM:646.9
MESH:D010922
MESH:D011248
NCI:C26857
NCI:C27619
NCI:C34941
NCI:C35169
SNOMEDCT_US_2016_03_01:125586008
SNOMEDCT_US_2016_03_01:156069003
SNOMEDCT_US_2016_03_01:156097009
SNOMEDCT_US_2016_03_01:156123001
SNOMEDCT_US_2016_03_01:156131006
SNOMEDCT_US_2016_03_01:172422001
SNOMEDCT_US_2016_03_01:173300003
SNOMEDCT_US_2016_03_01:198881004
SNOMEDCT_US_2016_03_01:199152008
SNOMEDCT_US_2016_03_01:23288008
SNOMEDCT_US_2016_03_01:267293009
SNOMEDCT_US_2016_03_01:267311008
SNOMEDCT_US_2016_03_01:267314000
SNOMEDCT_US_2016_03_01:90821003
UMLS_CUI:C0032045
UMLS_CUI:C0032962
UMLS_CUI:C0151864
UMLS_CUI:C1335423
disease_ontology
DOID:780
placenta disease
end stage renal disease
disease_ontology
DOID:783
end stage renal failure
EFO:0003884
ICD10CM:N18.9
ICD9CM:585.6
MESH:D007676
NCI:C9438
SNOMEDCT_US_2016_03_01:155856009
SNOMEDCT_US_2016_03_01:197654000
SNOMEDCT_US_2016_03_01:197655004
SNOMEDCT_US_2016_03_01:197755007
SNOMEDCT_US_2016_03_01:46177005
SNOMEDCT_US_2016_03_01:90688005
UMLS_CUI:C0022661
CKD
CRF
chronic kidney failure
chronic renal disease
chronic renal failure syndrome
renal failure - chronic
disease_ontology
DOID:784
chronic kidney disease
A substance abuse that involves the recurring use of cocaine despite negative consequences.
ICD10CM:F14.1
ICD9CM:305.6
ICD9CM:305.60
MESH:D019970
SNOMEDCT_US_2016_03_01:78267003
UMLS_CUI:C0009171
disease_ontology
DOID:809
cocaine abuse
MESH:D015356
NCI:C34978
SNOMEDCT_US_2016_03_01:232035005
UMLS_CUI:C0035302
Retinal artery occlusion (disorder)
disease_ontology
DOID:8483
retinal artery occlusion
A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide.
DOID:11894
DOID:11895
DOID:29
DOID:766
ICD10CM:J98.4
MESH:D008171
NCI:C3198
SNOMEDCT_US_2016_03_01:196164004
SNOMEDCT_US_2016_03_01:19829001
SNOMEDCT_US_2016_03_01:266374002
UMLS_CUI:C0024115
disease_ontology
DOID:850
Updating out dated CUI and removing lung abscess as a synonym.
lung disease
A gastrointestinal system cancer that is located_in the oral cavity.
DOID:0050627
DOID:8617
DOID:9049
DOID:9055
ICD10CM:C04
ICD10CM:C04.0
ICD10CM:C04.1
ICD10CM:C04.9
ICD9CM:144
ICD9CM:144.0
ICD9CM:144.1
ICD9CM:144.9
NCI:C9318
SNOMEDCT_US_2016_03_01:187652003
SNOMEDCT_US_2016_03_01:187653008
SNOMEDCT_US_2016_03_01:187656000
SNOMEDCT_US_2016_03_01:363385007
SNOMEDCT_US_2016_03_01:93672006
SNOMEDCT_US_2016_03_01:93802007
SNOMEDCT_US_2016_03_01:93860002
UMLS_CUI:C0153368
UMLS_CUI:C0153369
UMLS_CUI:C0496758
malignant neoplasm of anterior portion of floor of mouth
malignant neoplasm of floor of mouth
malignant neoplasm of lateral floor of mouth
malignant neoplasm of lateral portion of floor of mouth
malignant tumor of anterior floor of mouth (disorder)
malignant tumor of lateral floor of mouth (disorder)
malignant tumor of the Floor of the Mouth
disease_ontology
DOID:8618
oral cavity cancer
A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system.
ICD10CM:G00-G99
ICD10CM:G98
ICD10CM:G98.8
ICD9CM:349.9
MESH:D009422
NCI:C26835
SNOMEDCT_US_2016_03_01:118940003
SNOMEDCT_US_2016_03_01:154981003
SNOMEDCT_US_2016_03_01:155262005
SNOMEDCT_US_2016_03_01:192641002
SNOMEDCT_US_2016_03_01:267679005
SNOMEDCT_US_2016_03_01:286946008
UMLS_CUI:C0027765
disease_ontology
DOID:863
nervous system disease
DOID:8648
DOID:8779
DOID:8900
DOID:8940
DOID:8999
DOID:9058
DOID:9068
DOID:9196
ICD10CM:C01
ICD10CM:C02.0
ICD10CM:C02.1
ICD10CM:C02.2
ICD10CM:C02.4
ICD10CM:C02.9
ICD9CM:141
ICD9CM:141.0
ICD9CM:141.1
ICD9CM:141.2
ICD9CM:141.3
ICD9CM:141.5
ICD9CM:141.6
ICD9CM:141.9
MESH:D014062
NCI:C3524
NCI:C9345
SNOMEDCT_US_2016_03_01:187632004
SNOMEDCT_US_2016_03_01:187633009
SNOMEDCT_US_2016_03_01:187636001
SNOMEDCT_US_2016_03_01:187637005
SNOMEDCT_US_2016_03_01:187638000
SNOMEDCT_US_2016_03_01:187642002
SNOMEDCT_US_2016_03_01:187644001
SNOMEDCT_US_2016_03_01:187646004
SNOMEDCT_US_2016_03_01:363375006
SNOMEDCT_US_2016_03_01:363376007
SNOMEDCT_US_2016_03_01:363377003
SNOMEDCT_US_2016_03_01:371974006
SNOMEDCT_US_2016_03_01:93687001
SNOMEDCT_US_2016_03_01:93773005
SNOMEDCT_US_2016_03_01:93848003
SNOMEDCT_US_2016_03_01:93868009
SNOMEDCT_US_2016_03_01:94100005
SNOMEDCT_US_2016_03_01:94101009
SNOMEDCT_US_2016_03_01:94134006
UMLS_CUI:C0153349
UMLS_CUI:C0153350
UMLS_CUI:C0153351
UMLS_CUI:C0153356
UMLS_CUI:C0474963
UMLS_CUI:C0496755
UMLS_CUI:C0684333
Tongue neoplasm malignant stage Unspecified
malignant neoplasm of anterior 2/3 of tongue unspecified (disorder)
malignant neoplasm of anterior two-thirds of tongue, part unspecified
malignant neoplasm of base of tongue
malignant neoplasm of border of tongue
malignant neoplasm of dorsal surface of tongue
malignant neoplasm of dorsal tongue NOS
malignant neoplasm of dorsum of tongue NOS (disorder)
malignant neoplasm of fixed part of tongue NOS
malignant neoplasm of fixed part of tongue NOS (disorder)
malignant neoplasm of junctional zone of tongue
malignant neoplasm of lingual tonsil
malignant neoplasm of mobile part of tongue NOS
malignant neoplasm of other sites of tongue
malignant neoplasm of other sites of tongue (disorder)
malignant neoplasm of tip and lateral border of tongue
malignant neoplasm of tip and/or lateral border of tongue
malignant neoplasm of tongue
malignant neoplasm of tongue NOS
malignant neoplasm of tongue NOS (disorder)
malignant neoplasm of tongue, NOS
malignant neoplasm of tongue, tip and lateral border (disorder)
malignant neoplasm of ventral surface of tongue
malignant neoplasm of ventral tongue surface NOS (disorder)
malignant tumor of Posterior Tongue
malignant tumor of anterior two-thirds of tongue (disorder)
malignant tumor of base of tongue (disorder)
malignant tumor of lingual tonsil
malignant tumor of lingual tonsil (disorder)
malignant tumor of mobile part of tongue
malignant tumor of tongue (disorder)
disease_ontology
DOID:8649
tongue cancer
A vascular disease that is located_in a vein.
ICD10CM:I82
ICD9CM:453
SNOMEDCT_US_2016_03_01:195435006
UMLS_CUI:C0155774
disease_ontology
DOID:866
vein disease
A nervous system disease that is located_in nerves or nerve cells.
ICD10CM:G62.9
NCI:C4731
SNOMEDCT_US_2016_03_01:193167000
SNOMEDCT_US_2016_03_01:264554005
SNOMEDCT_US_2016_03_01:277317008
SNOMEDCT_US_2016_03_01:277878001
SNOMEDCT_US_2016_03_01:386033004
SNOMEDCT_US_2016_03_01:42658009
UMLS_CUI:C0442874
peripheral neuropathy
disease_ontology
DOID:870
neuropathy
DOID:14750
DOID:8711
DOID:9137
ICD10CM:Q85.00
ICD10CM:Q85.01
ICD10CM:Q85.02
ICD9CM:237.7
ICD9CM:237.70
ICD9CM:237.71
ICD9CM:237.72
MESH:C537392
MESH:D009456
MESH:D016518
MESH:D017253
NCI:C3273
NCI:C3274
NCI:C6727
OMIM:101000
OMIM:162200
OMIM:162210
OMIM:162260
OMIM:162270
ORDO:636
ORDO:637
ORDO:93921
SNOMEDCT_US_2016_03_01:154642000
SNOMEDCT_US_2016_03_01:19133005
SNOMEDCT_US_2016_03_01:700060008
SNOMEDCT_US_2016_03_01:700061007
SNOMEDCT_US_2016_03_01:81669005
SNOMEDCT_US_2016_03_01:92503002
SNOMEDCT_US_2016_03_01:92824003
UMLS_CUI:C0027831
UMLS_CUI:C0027832
UMLS_CUI:C0162678
UMLS_CUI:C0220695
Acoustic neurofibromatosis
Neurofibromatosis 1
Recklinghausen's neurofibromatosis
central Neurofibromatosis
neurofibromatosis type 1
neurofibromatosis type 2
neurofibromatosis type 4
neurofibromatosis type IV
peripheral Neurofibromatosis
type IV neurofibromatosis of riccardi
von Reklinghausen disease
disease_ontology
DOID:8712
Xref MGI.
OMIM mapping confirmed by DO. [SN].
neurofibromatosis
A pneumonia involving inflammation of the lungs caused by bacteria.
DOID:13815
ICD10CM:J15.9
ICD9CM:482.9
MESH:D018410
NCI:C26704
SNOMEDCT_US_2016_03_01:155553007
SNOMEDCT_US_2016_03_01:195891009
SNOMEDCT_US_2016_03_01:195892002
SNOMEDCT_US_2016_03_01:53084003
UMLS_CUI:C0004626
Pneumonia due to other gram-negative bacteria
gram-negative pneumonia
disease_ontology
DOID:874
bacterial pneumonia
ICD10CM:N84.0
ICD9CM:621.0
NCI:C3662
SNOMEDCT_US_2016_03_01:11314008
SNOMEDCT_US_2016_03_01:266659005
UMLS_CUI:C0156369
endometrial/uterine polyp
polyp of Endometrium
polyp of corpus uteri
polyp of the Uterus
polyp, uterus
disease_ontology
DOID:9042
polyp of corpus uteri
A glucose metabolism disease characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.
ICD10CM:E08-E13
ICD10CM:E11
ICD9CM:250
MESH:D003920
NCI:C2985
SNOMEDCT_US_2016_03_01:154671004
SNOMEDCT_US_2016_03_01:191044006
SNOMEDCT_US_2016_03_01:267467004
SNOMEDCT_US_2016_03_01:73211009
UMLS_CUI:C0011849
disease_ontology
DOID:9351
diabetes mellitus
A diabetes mellitus that involves high blood glucose resulting from cells fail to use insulin properly.
EFO:0001360
ICD10CM:E11
KEGG:04930
MESH:D003924
NCI:C26747
OMIM:125853
OMIM:601283
OMIM:601407
OMIM:603694
OMIM:608036
SNOMEDCT_US_2016_03_01:154672006
SNOMEDCT_US_2016_03_01:190323008
SNOMEDCT_US_2016_03_01:190384004
SNOMEDCT_US_2016_03_01:267468009
SNOMEDCT_US_2016_03_01:44054006
UMLS_CUI:C0011860
NIDDM
non-insulin-dependent diabetes mellitus
type II diabetes mellitus
disease_ontology
DOID:9352
Xref MGI.
OMIM mapping confirmed by DO. [SN].
type 2 diabetes mellitus
A central nervous system disease that is located_in the brain.
DOID:8510
ICD10CM:G93.40
ICD10CM:G93.9
ICD9CM:348.3
ICD9CM:348.30
ICD9CM:348.9
MESH:D001927
NCI:C26920
NCI:C96413
SNOMEDCT_US_2016_03_01:155053002
SNOMEDCT_US_2016_03_01:193051008
SNOMEDCT_US_2016_03_01:193059005
SNOMEDCT_US_2016_03_01:76011009
SNOMEDCT_US_2016_03_01:81308009
UMLS_CUI:C0006111
UMLS_CUI:C0085584
encephalopathy
disease_ontology
DOID:936
brain disease
MESH:D019586
NCI:C84791
SNOMEDCT_US_2016_03_01:155052007
SNOMEDCT_US_2016_03_01:267701004
SNOMEDCT_US_2016_03_01:271719001
SNOMEDCT_US_2016_03_01:28073009
UMLS_CUI:C0151740
Raised intracranial pressure
disease_ontology
DOID:9428
intracranial hypertension
MESH:D009455
NCI:C3272
SNOMEDCT_US_2016_03_01:115242003
SNOMEDCT_US_2016_03_01:134214003
SNOMEDCT_US_2016_03_01:189947001
SNOMEDCT_US_2016_03_01:404029005
SNOMEDCT_US_2016_03_01:89084002
UMLS_CUI:C0027830
disease_ontology
DOID:962
neurofibroma
biome
environmental system
geographic location
A reference to a place on the Earth, by its name or by its geographical location.
geographic location
system process
circulatory system process
response to stress
defense response
inflammatory response
respiratory gaseous exchange
blood coagulation
hemostasis
behavior
feeding behavior
blood circulation
biological_process
multicellular organismal process
developmental process
growth
locomotion
symbiosis, encompassing mutualism through parasitism
interspecies interaction between organisms
coagulation
regulation of body fluid levels
response to stimulus
interaction with symbiont
multi-organism process
multi-organism behavior
acquisition of nutrients from other organism during symbiotic interaction
acquisition of nutrients from symbiont
biological regulation
regulation of biological quality
parasitism
mutualism
commensalism
hypertensive phenotype
The presence of chronic increased pressure in the systemic arterial system.
Hypertension
Amanda Hicks
A blood pressure measurement datum that is a quality measure of some diastolic blood pressure
diastolic blood pressure measurement datum
A blood pressure measurement datum that is a quality measure of some systolic blood pressure
Amanda Hicks
systolic blood pressure measurement datum
120.0
A systolic blood pressure measurement datum that is about a blood pressure that inheres in an adult with a measurement value that is equal to or above some specified threshold for adults
elevated adult systolic blood pressure measurement datum
2
A phenotype of hypertension that has been documented
Amanda Hicks
documented hypertensive phenotype
Amanda Hicks
A human who is equal to or older than 18 years old
adult over 18 years of age
An elevated blood pressure phenotype of systolic blood pressure that is above some specifed threshold
Amanda Hicks
elevated systolic phenotype
Amanda Hicks
A systolic blood pressure measurement datum with a measurement value that is equal to or above some specified threshold
elevated systolic blood pressure measurement datum
A phenotype of blood pressure that is above some specified threshold
Amanda Hicks
elevated blood pressure phenotype
A blood pressure measurement datum with a measurement value that is equal to or above some specified threshold
elevated blood pressure measurement datum
An elevated blood pressure phenotype of diastolic blood pressure that is above some specifed threshold
Amanda Hicks
elevated diastolic phenotype
A diagnosis that asserts of some patient that they have a disposition to chronically elevated blood pressure
diagnosis of hypertension
130.0
139.0
2017 Guideline for High Blood Pressure in Adults
http://www.onlinejacc.org/content/71/19/e127?_ga=2.55616109.754894593.1553089039-383350264.1553089039
An elevated adult diastolic blood pressure measurement datum that is quality measurement of a diastolic blood pressure is equal to above 120 mm Hg and equal to or less than 139 mm Hg
Amanda Hicks
stage 1 elevated adult systolic blood pressure meaurement datum per ACC 2017 guidelines
A diastolic blood pressure measurement datum with a measurement value that is equal to or above some specified threshold
elevated diastolic blood pressure measurement datum
80.0
Amanda Hicks
An elevated diastolic blood pressure measurement datum that is quality measurement of a diastolic blood pressure that inheres in an adult with a measurement value that is equal to or above some specified threshold for adults
elevated adult diastolic blood pressure measurement datum
80.0
89.0
2017 Guideline for High Blood Pressure in Adults
http://www.onlinejacc.org/content/71/19/e127?_ga=2.55616109.754894593.1553089039-383350264.1553089039
An elevated adult diastolic blood pressure measurement datum that is quality measurement of a diastolic blood pressure is equal to above 80 mm Hg and equal to or less than 89 mm Hg
stage 1 elevated adult diastolic blood pressure measurement datum per 2017 guidelines
90.0
stage 2 elevated adult diastolic blood pressure measurement datum per 2017 guidelines
140.0
stage 2 elevated adult systolic blood pressure meaurement datum per ACC 2017 guidelines
80.0
129.0
120–129 mm Hg and <80 mm Hg
elevated adult blood pressure measurement datum per 2017 guidelines
130–139 mm Hg or 80–89 mm Hg
stage 1 adult blood pressure measurement datum per 2017 guidelines
stage 2 adult blood pressure measurement datum per 2017 guidelines
18.0
An age measurement datum that is about a human being has a measurement value equal to or greater than 18 years
Amanda Hicks
adult over 18 years of age measurement datum
conditional specification
a directive information entity that specifies what should happen if the trigger condition is fulfilled
PlanAndPlannedProcess Branch
OBI branch derived
OBI_0000349
conditional specification
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was
proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and
Cristian Cocos, and subsequently moved to IAO where the objective for
which the original term was defined was satisfied with the definition
of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
measurement unit label
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: Alan Ruttenberg
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
OBI_0000217
objective specification
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
OBI_0000013
group:OBI
narrative object
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
Alan Ruttenberg
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
http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n
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.
datum label
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: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Chris Stoeckert
PERSON: Melanie Courtot
GROUP: OBI
software
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
person:Alan Ruttenberg
person:Chris Stoeckert
OBI_0000159
group:OBI
journal article
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.
PERSON: Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
information carrier
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
Person: Alan Ruttenberg
model number
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.
person:Alan Ruttenberg
person:Chris Stoeckert
OBI_0000058
group:OBI
programming language
data item
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
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
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
data item
symbol
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
PERSON: James A. Overton
PERSON: Jonathan Rees
based on Oxford English Dictionary
symbol
numeral
A symbol that denotes a number.
PERSON: Jonathan Rees
numeral
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.
An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
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.
PERSON: Chris Stoeckert
OBI_0000142
information content entity
integer numeral
a numeral that denotes an integer
PERSON: Jonathan Rees
integer numeral
1
1
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.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
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
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
directive information content entity
directive information entity
time trigger
revisit?
PlanAndPlannedProcess Branch
OBI branch derived
OBI_0000331
time trigger
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
person:Chris Stoeckert
OBI_0000123
group:OBI
dot plot
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
person:Alan Ruttenberg
person:Allyson Lister
OBI_0000240
group:OBI
graph
rule
example to be added
a rule is an executable which guides, defines, restricts actions
MSI
PRS
OBI_0500021
PRS
rule
contour plot
Contour plot of SSC-H, FSC-H, and FL1-H.
generically_dependent_continuants
person:Allyson Lister
person:Chris Stoeckert
OBI_0000246
group:Flow Cytometry community
contour plot
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
PlanAndPlannedProcess Branch
OBI_0000270
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
algorithm
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
person:Alan Ruttenberg
person:Chris Stoeckert
OBI_0000199
group:OBI
software 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)
PERSON:Bill Bug
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
curation status specification
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.
person:Allyson Lister
person:Chris Stoeckert
OBI_0000179
group:Flow Cytometry community
density plot
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.
2009-03-16: 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.
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
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
PERSON:Chris Stoeckert
GROUP: OBI
OBI_0000099
report
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.
person:Alan Ruttenberg
person:Chris Stoeckert
OBI_0000039
group:OBI
source code module
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"
PERSON: Alan Ruttenberg
PlanAndPlannedProcess Branch
OBI branch derived
OBI_0000187
data format specification
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.
person:Allyson Lister
person:Chris Stoeckert
OBI_0000042
group:OBI
data set
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.
person:Alan Ruttenberg
person:Allyson
person:Chris Stoeckert
OBI_0000030
group:OBI
image
data about an ontology part is a data item about a part of an ontology, for example a term
Person:Alan Ruttenberg
data about an ontology part
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
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.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Alan Ruttenberg
OBI Plan and Planned Process branch
OBI_0000344
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
plan specification
measurement datum
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?
person:Chris Stoeckert
OBI_0000305
group:OBI
measurement datum
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
GROUP: IAO
version number
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 :-)
GROUP: IAO
serial number
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.
GROUP: IAO
batch number
lot 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
conclusion textual entity
that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
2009/10/23 Alan Ruttenberg: We need to work on the definition still
Person:Alan Ruttenberg
conclusion textual entity
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.
GROUP: IAO
material information bearer
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
PERSON:Melanie Courtot
GROUP:OBI
histogram
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.
PERSON:Chris Stoeckert
PERSON:James Malone
PERSON:Melanie Courtot
GROUP:OBI
heatmap
Venn diagram
A Venn diagram is a report graph showing all hypothetically possible
logical relations between a finite collection of sets.
PERSON:Chris Stoeckert
PERSON:James Malone
PERSON:Melanie Courtot
WEB: http://en.wikipedia.org/wiki/Venn_diagram
Venn diagram
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.
PERSON:Chris Stoeckert
PERSON:James Malone
PERSON:Melanie Courtot
WEB: http://en.wikipedia.org/wiki/Dendrogram
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.
PERSON:Chris Stoeckert
PERSON:James Malone
PERSON:Melanie Courtot
scattergraph
WEB: http://en.wikipedia.org/wiki/Scatterplot
scatter plot
A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
PERSON:Alan Ruttenberg
PERSON:Joanne Luciano
PERSON:Melanie Courtot
WEB: http://en.wiktionary.org/wiki/photograph
photograph
photographic print
A photographic print is a material entity upon which a photograph generically depends.
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
photographic print
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.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
obsolescence reason specification
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.
PERSON: Lawrence Hunter
text
textual entity
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
PERSON: Lawrence Hunter
citation
author identification
L. Hunter
A textual entity intended to identify a particular author
PERSON: Lawrence Hunter
author identification
institutional identification
University of Colorado Denver School of Medicine
A textual entity intended to identify a particular institution
PERSON: Lawrence Hunter
institutional identification
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
PERSON: Lawrence Hunter
caption
document title
Textual characteristics of traditional and Open Access scientific journals are similar
A textual entity that names a document
PERSON: Lawrence Hunter
document title
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
PERSON: Lawrence Hunter
table
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
PERSON: Lawrence Hunter
table of abbreviations
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.
PERSON: Lawrence Hunter
figure
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
PERSON: Lawrence Hunter
diagram
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
PERSON: Lawrence Hunter
document
publication
A journal article or book
A document that has been accepted by a publisher
PERSON: Lawrence Hunter
publication
publication about an investigation
Most scientific journal articles
A publication that is about an investigation
PERSON: Lawrence Hunter
scientific publication
publication about an investigation
patent
US Patent 6,449,603
A document that has been accepted by a patent authority
PERSON: Lawrence Hunter
patent
document part
An abstract, introduction, method or results section.
an information content entity that is part of a document
PERSON: Lawrence Hunter
document part
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.
PERSON: Lawrence Hunter
abstract
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)
PERSON: Lawrence Hunter
background
introduction
introduction to a publication about an investigation
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
PERSON: Lawrence Hunter
experimental
experimental procedures
experimental section
methods
methods section