None
These are the terms that are improted for FOVT to describe vertebrate traits.
FuTRES Ontology of Vertebrate Traits
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred term
example
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>
IAO:0000116
uberon
editor_note
true
editor_note
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 https://github.com/information-artifact-ontology/IAO/issues/115.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
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
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
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 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
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
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
A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
David Osumi-Sutherland
#40
VFB
2018-09-21T16:43:39Z
Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
may be identical to
Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
Chris Mungall, Jie Zheng
https://github.com/geneontology/go-ontology/issues/15532
https://github.com/information-artifact-ontology/ontology-metadata/issues/32
GO ontology
scheduled for obsoletion on or after
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
term replaced by
tooth SubClassOf 'never in taxon' value 'Aves'
S never_in_taxon T iff: S SubClassOf in_taxon only not T
S never_in_taxon T iff: S SubClassOf in_taxon only not T.
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
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y)
RO:0002161
uberon
never_in_taxon
true
true
never_in_taxon
never in taxon
never_in_taxon
S never_in_taxon T iff: S SubClassOf in_taxon only not T.
PMID:20973947
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
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
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.
http://purl.org/dc/elements/1.1/description
uberon
dc-description
true
dc-description
An account of the content of the resource.
Description
Description
description
Typically, a Title will be a name by which the resource is
formally known.
http://purl.org/dc/elements/1.1/title
uberon
dc-title
true
dc-title
A name given to the resource.
Title
Title
title
Mark Miller
2018-05-11T13:47:29Z
http://purl.org/dc/terms/license
uberon
dcterms-license
true
dcterms-license
license
has_broad_synonym
database_cross_reference
has_exact_synonym
has_related_synonym
is part of
is part of
my brain is part of my body (continuant parthood, two material entities)
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)
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)
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.
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
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'.
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part_of
BFO:0000050
external
oba
protein
quality
uberon
part_of
part_of
part of
part of
part_of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
has part
my body has part my brain (continuant parthood, two material entities)
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)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
this year has part this day (occurrent parthood)
Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2.
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.
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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
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'.
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
has_part
BFO:0000051
chebi_ontology
external
oba
protein
quality
uberon
has_part
false
has_part
We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'.
has part
has part
has_part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
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
X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X).
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.
BFO:0000062
is preceded by
takes place after
uberon
preceded_by
preceded_by
preceded by
preceded by
preceded_by
is preceded by
SIO:000249
takes place after
Allen: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.
BFO:0000063
uberon
precedes
precedes
precedes
precedes
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
[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
BFO:0000067
uberon
contains_process
contains_process
contains process
contains process
x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer.
cjm
2009-07-31T02:15:46Z
BSPO:0000096
uberon
anterior_to
anterior_to
anterior to
anterior_to
x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
BSPO:cjm
x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer.
http://orcid.org/0000-0002-6601-2165
x distal to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
BSPO:0000097
uberon
distal_to
distal_to
distal to
distal_to
x distal to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
BSPO:cjm
x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
http://orcid.org/0000-0002-6601-2165
x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
BSPO:0000098
uberon
dorsal_to
dorsal_to
dorsal to
dorsal_to
x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
BSPO:cjm
x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
http://orcid.org/0000-0002-6601-2165
x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.
BSPO:0000099
caudal_to
uberon
posterior_to
posterior_to
posterior to
posterior_to
x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
BSPO:cjm
x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.
http://orcid.org/0000-0002-6601-2165
x proximal to y iff x is closer to the point of attachment with the body than y.
x proximal_to y iff x is closer to the point of attachment with the body than y.
BSPO:0000100
uberon
proximal_to
proximal_to
proximal to
proximal_to
x proximal to y iff x is closer to the point of attachment with the body than y.
BSPO:cjm
x proximal_to y iff x is closer to the point of attachment with the body than y.
http://orcid.org/0000-0002-6601-2165
x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
BSPO:0000102
uberon
ventral_to
ventral_to
ventral to
ventral_to
x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
BSPO:cjm
x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
http://orcid.org/0000-0002-6601-2165
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
BSPO:0000107
uberon
deep_to
deep_to
deep to
deep_to
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
BSPO:cjm
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
BSPO:0000108
uberon
superficial_to
superficial_to
superficial to
superficial_to
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
BSPO:cjm
X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
BSPO:0000120
uberon
in_left_side_of
in_left_side_of
in left side of
in_left_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
BSPO:PATO_mtg_2009
X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
BSPO:PATO_mtg_2009
X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
BSPO:0000121
uberon
in_right_side_of
in_right_side_of
in right side of
in_right_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
BSPO:PATO_mtg_2009
X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
BSPO:PATO_mtg_2009
X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion.
X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
BSPO:0000122
uberon
in_posterior_side_of
in_posterior_side_of
in posterior side of
in_posterior_side_of
X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion.
BSPO:PATO_mtg_2009
X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
BSPO:PATO_mtg_2009
X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion.
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
BSPO:0000123
uberon
in_anterior_side_of
in_anterior_side_of
in anterior side of
in_anterior_side_of
X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion.
BSPO:PATO_mtg_2009
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
BSPO:PATO_mtg_2009
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion.
BSPO:0000124
uberon
in_proximal_side_of
in_proximal_side_of
in proximal side of
in_proximal_side_of
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
BSPO:PATO_mtg_2009
x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion.
BSPO:PATO_mtg_2009
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion.
BSPO:0000125
uberon
in_distal_side_of
in_distal_side_of
in distal side of
in_distal_side_of
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
BSPO:PATO_mtg_2009
x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion.
BSPO:PATO_mtg_2009
X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure
X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure.
BSPO:0000126
uberon
in_lateral_side_of
in_lateral_side_of
in lateral side of
in_lateral_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure
UBERON:cjm
X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure.
https://orcid.org/0000-0002-6601-2165
X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y.
BSPO:0001106
uberon
proximalmost_part_of
proximalmost_part_of
proximalmost part of
proximalmost_part_of
X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y
https://orcid.org/0000-0002-6601-2165
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y.
https://orcid.org/0000-0002-6601-2165
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
x immediately deep to y iff x deep_to y and x is contiguous with y.
BSPO:0001107
uberon
immediately_deep_to
immediately_deep_to
immediately deep to
immediately_deep_to
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
http://orcid.org/0000-0002-6601-2165
x immediately deep to y iff x deep_to y and x is contiguous with y.
BSPO:curators
X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y
X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y.
BSPO:0001108
uberon
distalmost_part_of
distalmost_part_of
distalmost part of
distalmost_part_of
X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y
https://orcid.org/0000-0002-6601-2165
X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y.
https://orcid.org/0000-0002-6601-2165
BSPO:0001113
uberon
preaxialmost_part_of
preaxialmost_part_of
preaxialmost part of
preaxialmost_part_of
BSPO:0001115
uberon
postaxialmost_part_of
postaxialmost_part_of
postaxialmost part of
postaxialmost_part_of
X intersects median plane of iff X crosses the midine plane of Y.
X intersects_median_plane of iff X crosses the midine plane of Y.
BSPO:0005001
uberon
intersects_midsagittal_plane_of
intersects_midsagittal_plane_of
intersects midsagittal plane of
intersects_midsagittal_plane_of
x immediately superficial to y iff x superficial to y and x is contiguous with y.
BSPO:0015014
uberon
immediately_superficial_to
immediately_superficial_to
immediately superficial to
immediately_superficial_to
x immediately superficial to y iff x superficial to y and x is contiguous with y.
BSPO:curators
X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion.
BSPO:0015101
uberon
in_dorsal_side_of
in_dorsal_side_of
in dorsal side of
in_dorsal_side_of
X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion.
BSPO:cjm
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
inverse of the relation 'denotes'
Person: Jie Zheng, Chris Stoeckert, Mike Conlon
denoted by
has_specified_input
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
is_specified_input_of
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
Alan Ruttenberg
PERSON:Bjoern Peters
is_specified_input_of
is_specified_input_of
has_specified_output
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
is_specified_output_of
is_specified_output_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
Alan Ruttenberg
PERSON:Bjoern Peters
is_specified_output_of
achieves_planned_objective
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
BP, AR, PPPB branch
PPPB branch derived
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
achieves_planned_objective
objective_achieved_by
This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
OBI
OBI
objective_achieved_by
inheres in
this fragility inheres in this vase
this red color inheres in this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
RO:0000052
oba
inheres_in
inheres_in
characteristic of
inheres in
inheres in
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
RO:0000053
uberon
bearer_of
bearer_of
bearer of
bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
RO:0000056
uberon
participates_in
participates_in
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
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
function of
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
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
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
has function
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
RO:0000086
uberon
has_quality
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
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
inverse of has disposition
disposition of
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
RO:0001015
uberon
location_of
location_of
location of
location_of
contained in
RO:0001019
uberon
contains
contains
contains
contains
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
RO:0001025
uberon
located_in
located_in
located in
located_in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
RO:0002000
uberon
boundary_of
boundary_of
2D boundary of
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
RO:0002002
uberon
has_boundary
has_boundary
has 2D boundary
has boundary
RO:0002005
nerve supply
uberon
innervated_by
innervated_by
http://code.google.com/p/obo-relations/issues/detail?id=6
innervated_by
nerve supply
FMA:85999
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
RO:0002007
uberon
bounding_layer_of
bounding_layer_of
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
bounding layer of
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
has regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
has positive regulatory component activity
has component activity
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
has component process
directly regulated by
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
directly negatively regulated by
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
GOC:dos
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
directly positively regulated by
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
GOC:dos
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
has effector activity
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
GOC:dos
before or simultaneous with
Relation between occurrents, shares start and end boundaries.
RO:0002082
coincides_with
is_equal_to
uberon
simultaneous_with
simultaneous_with
simultaneous with
Relation between occurrents, shares start and end boundaries.
Allen:is_equal_to
https://orcid.org/0000-0002-6601-2165
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y).
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
RO:0002087
directly preceded by
is directly preceded by
is immediately preceded by
starts_at_end_of
uberon
immediately_preceded_by
immediately_preceded_by
immediately preceded by
immediately_preceded_by
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
SIO:000251
is immediately preceded by
SIO:000251
immediately precedes
x overlaps y if and only if there exists some z such that x has part z and z part of y
BFO_0000051 some (BFO_0000050 some ?Y)
RO:0002131
uberon
overlaps
overlaps
overlaps
overlaps
true
Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.
T innervates some R
Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
RO:0002134
uberon
innervates
innervates
http://code.google.com/p/obo-relations/issues/detail?id=6
innervates
X continuous_with Y if and only if X and Y share a fiat boundary.
RO:0002150
uberon
continuous_with
continuous_with
continuous with
continuous_with
RO:0002158
uberon
homologous_to
homologous_to
S only_in_taxon T iff: S SubClassOf in_taxon only T.
x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
RO:0002160
uberon
only_in_taxon
only_in_taxon
only in taxon
S only_in_taxon T iff: S SubClassOf in_taxon only T.
PMID:20973947
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
RO:0002162
uberon
in_taxon
in_taxon
in taxon
Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
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
RO:0002170
uberon
connected_to
connected_to
Connection does not imply overlaps.
connected to
connected to
Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
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.
this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)
RO:0002176
uberon
connects
connects
connects
connects
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
RO:0002177
uberon
attaches_to_part_of
attaches_to_part_of
attached to part of
attaches_to_part_of
true
true
Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
relation between an artery and the structure is supplies with blood.
RO:0002178
arterial supply of
uberon
supplies
supplies
source: FMA
supplies
arterial supply of
FMA:86003
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.
RO:0002179
drains blood from
drains from
uberon
drains
drains
source: Wikipedia
drains
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.
RO:0002180
uberon
has_component
has_component
has component
has component
has_component
x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
Terry Meehan
RO:0002202
uberon
develops_from
develops_from
This is the transitive form of the develops from relation
develops from
develops from
develops_from
inverse of develops from
RO:0002203
uberon
develops_into
develops_into
develops into
develops_into
Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
RO:0002207
uberon
directly_develops_from
directly_develops_from
directly develops from
inverse of directly develops from
directly develops into
process(P1) regulates process(P2) iff:Â P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
RO:0002211
regulates
regulates
regulates
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
RO:0002212
negatively_regulates
negatively regulates
negatively regulates
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
RO:0002213
positively_regulates
positively regulates
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.
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:0002215
protein
uberon
capable_of
false
capable_of
capable of
capable of
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.
RO:0002216
uberon
capable_of_part_of
capable_of_part_of
capable of part of
capable of part of
true
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
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y.
RO:0002219
uberon
surrounded_by
surrounded_by
surrounded by
surrounded_by
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y.
https://orcid.org/0000-0002-6601-2165
x adjacent to y if and only if x and y share a boundary.
x adjacent_to y iff: x and y share a boundary.
RO:0002220
uberon
adjacent_to
adjacent_to
adjacent to
adjacent to
adjacent_to
inverse of surrounded by
inverse of surrounded_by.
RO:0002221
uberon
surrounds
surrounds
surrounds
surrounds
inverse of surrounded_by.
https://orcid.org/0000-0002-6601-2165
temporally related to
Relation between occurrents, shares a start boundary with.
inverse of starts with
RO:0002223
uberon
starts
starts
starts
starts
Relation between occurrents, shares a start boundary with.
Allen:starts
https://orcid.org/0000-0002-6601-2165
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.
RO:0002224
uberon
starts_with
starts_with
starts with
starts with
x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
RO:0002225
uberon
develops_from_part_of
develops_from_part_of
develops from part of
x develops_in y if x is located in y whilst x is developing
RO:0002226
uberon
develops_in
develops_in
This relation take from EHDAA2 - precise semantics yet to be defined
develops in
Relation between occurrents, shares an end boundary with.
inverse of ends with
RO:0002229
finishes
uberon
ends
ends
ends
ends
Relation between occurrents, shares an end boundary with.
Allen:starts
ZFS:finishes
https://orcid.org/0000-0002-6601-2165
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.
RO:0002230
uberon
ends_with
ends_with
ends with
ends with
x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
has start location
x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
has end location
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
has output
x has developmental contribution from y iff x has some part z such that z develops from y
RO:0002254
uberon
has_developmental_contribution_from
has_developmental_contribution_from
has developmental contribution from
has developmental contribution from
inverse of has developmental contribution from
RO:0002255
uberon
developmentally_contributes_to
developmentally_contributes_to
developmentally contributes to
t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T
RO:0002256
uberon
developmentally_induced_by
developmentally_induced_by
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
developmentally induced by
developmentally_induced_by
t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
GO:0001759
Inverse of developmentally induced by
developmentally induces
Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
RO:0002258
uberon
developmentally_preceded_by
developmentally_preceded_by
developmentally preceded by
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
acts upstream of
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
acts upstream of or within
x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
RO:0002285
uberon
developmentally_replaces
developmentally_replaces
developmentally replaces
developmentally_replaces
Inverse of developmentally preceded by
developmentally succeeded by
part of developmental precursor of
causally upstream of, positive effect
causally upstream of, negative effect
RO:0002314
oba
inheres_in_part_of
inheres_in_part_of
inheres in part -of
RO:0002322
adapted_for
uberon
confers_advantage_in
confers_advantage_in
confers advantage in
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
RO:0002328
uberon
functionally_related_to
functionally_related_to
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
RO:0002329
uberon
part_of_structure_that_is_capable_of
part_of_structure_that_is_capable_of
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
involved in
inverse of enables
enabled by
inverse of regulates
regulated by
inverse of negatively regulates
negatively regulated by
inverse of positively regulates
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
RO:0002350
uberon
member_of
member_of
member of
member of
has member is a mereological relation between a collection and an item.
SIO
RO:0002351
uberon
has_member
has_member
has member
has member
inverse of has input
RO:0002352
uberon
input_of
input_of
input of
inverse of has output
RO:0002353
uberon
output_of
output_of
output of
output of
a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
RO:0002371
uberon
attaches_to
attaches_to
attached to
attaches_to
m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
RO:0002372
uberon
has_muscle_origin
has_muscle_origin
The origin is the end of a muscle that attaches to the more fixed part of the skeleton, which is the proximal end in limb muscles
has muscle origin
We need to import uberon muscle to create a stricter domain constraint
m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
Wikipedia:Insertion_(anatomy)#Muscles
m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
RO:0002373
uberon
has_muscle_insertion
has_muscle_insertion
The insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscles
has muscle insertion
We need to import uberon muscle into RO to use as a stricter domain constraint
m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
Wikipedia:Insertion_(anatomy)
x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat
x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat.
RO:0002374
uberon
has_fused_element
has_fused_element
A single bone in one species may correspond to the fusion of two or more bones found as distinct elements in another. For example, tibiofibula has_fused_element tibia. A has_fused_element B does not imply that A has_part some B, rather than A has_part some B', where B' is not a subtype of B (because B is a distinct element but B' is a regional part) but has some evolutionary relationship to B.
derived from ancestral fusion of
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.
in branching relationship with
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.
RO:0002376
uberon
drains into
tributary_of
tributary_of
tributary of
tributary_of
drains into
dbpowl:drainsTo
x spatially_coextensive_with y if and inly if x and y have the same location
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
we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve
RO:0002380
uberon
branching_part_of
branching_part_of
branching part of
branching_part_of
x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
has developmental potential involving
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y.
RO:0002385
uberon
has_potential_to_developmentally_contribute_to
has_potential_to_developmentally_contribute_to
has potential to developmentally contribute to
x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
has potential to developmentally induce
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
x has the potential to develop into y iff x develops into y or if x is capable of developing into y.
RO:0002387
uberon
has_potential_to_develop_into
has_potential_to_develop_into
has potential to develop into
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y.
RO:0002388
uberon
has_potential_to_directly_develop_into
has_potential_to_directly_develop_into
has potential to directly develop into
inverse of upstream of
causally downstream of
immediately causally downstream of
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
causally upstream of
p is 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.
immediately causally upstream of
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.
causally upstream of or within
inverse of causally upstream of or within
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
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
involved in or involved in regulation of
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
is active in
true
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
GOC:cjm
GOC:dos
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.
RO:0002433
uberon
contributes_to_morphology_of
contributes_to_morphology_of
contributes to morphology of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
interacts with
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
molecularly interacts with
phosphorylates
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
directly regulates activity of
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
directly positively regulates activity of
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.
x composed_primarily_of y iff: more than half of the mass of x is made from parts of y.
RO:0002473
uberon
composed_primarily_of
composed_primarily_of
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.
has part that occurs in
true
relation between physical entity and a process or stage
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
RO:0002488
begins_to_exist_during
uberon
existence_starts_during
existence_starts_during
existence starts during
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
https://orcid.org/0000-0002-6601-2165
Relation between continuant and occurrent, such that c comes into existence at the start of p.
x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
RO:0002489
uberon
existence_starts_with
existence_starts_with
existence starts with
Relation between continuant and occurrent, such that c comes into existence at the start of p.
https://orcid.org/0000-0002-6601-2165
x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
existence overlaps
x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
RO:0002491
uberon
existence_starts_and_ends_during
existence_starts_and_ends_during
existence starts and ends during
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
RO:0002492
ceases_to_exist_during
uberon
existence_ends_during
existence_ends_during
existence ends during
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
https://orcid.org/0000-0002-6601-2165
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
RO:0002493
uberon
existence_ends_with
existence_ends_with
existence ends with
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
https://orcid.org/0000-0002-6601-2165
x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
RO:0002494
transforms from
uberon
transformation_of
transformation_of
transformation of
transforms from
SIO:000657
x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
RO:0002495
direct_transformation_of
immediately transforms from
uberon
immediate_transformation_of
immediate_transformation_of
immediate transformation of
direct_transformation_of
https://orcid.org/0000-0002-6601-2165
immediately transforms from
SIO:000658
x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
RO:0002496
uberon
existence_starts_during_or_after
existence_starts_during_or_after
existence starts during or after
x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
RO:0002497
uberon
existence_ends_during_or_before
existence_ends_during_or_before
existence ends during or before
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
causal relation between processes
causal relation between entities
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.
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
RO:0002551
uberon
has sekeletal support
has supporting framework
has_skeleton
has_skeleton
has skeleton
This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
http://orcid.org/0000-0002-6601-2165
causally influenced by
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
causally influences
A relation that holds between elements of a musculoskeletal system or its analogs.
biomechanically related to
m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.
m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.
RO:0002568
uberon
has_muscle_antagonist
has_muscle_antagonist
has muscle antagonist
m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.
Wikipedia:Antagonist_(muscle)
inverse of branching part of
RO:0002569
uberon
has_branching_part
has_branching_part
has branching part
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.
RO:0002571
uberon
lumen_of
lumen_of
lumen of
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
RO:0002572
uberon
luminal_space_of
luminal_space_of
luminal space of
inverse of has skeleton
RO:0002576
uberon
skeleton_of
skeleton_of
skeleton of
Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
directly regulates
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
has part structure that is capable 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.
causal relation between material entity and a process
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
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
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
Inverse of 'causal agent in process'
process has causal agent
Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
directly positively regulates
Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
directly negatively regulates
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
RO:0003000
uberon
produces
produces
produces
produces
a produced_by b iff some process that occurs_in b has_output a.
RO:0003001
uberon
produced_by
produced_by
produced by
produced by
produced_by
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
enables subfunction
acts upstream of or within, positive effect
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
acts upstream of, positive effect
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
acts upstream of, negative effect
causally upstream of or within, negative effect
causally upstream of or within, positive effect
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
regulates activity of
x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
uberon
anteriorly_connected_to
anteriorly connected to
x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
carries
uberon
channel_for
channel for
uberon
channels_from
channels_from
uberon
channels_into
channels_into
x is a conduit for y iff y passes through the lumen of x.
uberon
conduit_for
conduit for
x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.
uberon
distally_connected_to
distally connected to
x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
uberon
extends_fibers_into
extends_fibers_into
Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity.
uberon
filtered_through
Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed
filtered through
X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides.
uberon
in_central_side_of
in_central_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides.
BSPO:cjm
a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s.
add to RO
uberon
indirectly_supplies
indirectly_supplies
x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
uberon
posteriorly_connected_to
posteriorly connected to
x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
uberon
protects
protects
x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.
uberon
proximally_connected_to
proximally connected to
x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
uberon
sexually_homologous_to
sexually_homologous_to
c site_of p if c is the bearer of a disposition that is realized by a process that has p as part.
uberon
capable_of_has_part
site_of
site_of
uberon
subdivision_of
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
subdivision of
Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
uberon
synapsed_by
synapsed by
.
uberon
transitively_anteriorly_connected_to
transitively anteriorly connected to
.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
uberon
transitively_connected_to
transitively_connected to
.
uberon
transitively_distally_connected_to
transitively distally connected to
.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
.
uberon
transitively_proximally_connected_to
transitively proximally connected to
.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
sighting
A trip camera capture of an image of a jaguar is an observation, because it is "selected" by the camera as worthy of obsevation simply by virtue of moving in front of the camera.
Observing and recording the presence or absence of butterflies during a transect walk.
Seeing three pelicans flying overhead on Christmas day and report them as part of the Christmas Bird Count.
A process in which a person or machine sees or detects a material entity and selects it as worthy of observation, and which has as output an information content entity about the selected material entity.
This class replaces class bco_0000003, which was made obsolete because of identifier format.
We are having conversation with OBI developers about how this term relates to OBI:assay (). Is it equivalent, broader, narrower? What does it mean to be the input to an observation.
Biocode Commons Ontology Hackathon
An observing process is distinguished from a specimen collecting process in by having an information content entity as an output rather than a specimen. The information artifact may be written or recorded or just be stored in someone's head (specifically depenedent upon that person). In the context of a taxonomic inventory, an observing process may be called a sighting, which is an ad hoc reporting of, typically, a single taxon occurrence, usually motivated by rarity, individual interest in the taxon, or atypicality of circumstances.
observing process
the role borne by a bird during a Christmas Bird Count
A role that is borne by some material entity and is realized by the material entity being the input of an observing process.
This term replaced bco_0000046, which was made obsolete because of incorrect identifier format.
Biocode Commons Ontology Hackathon
material target of observation role
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.
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.
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.
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]
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.
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]
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]
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]
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.
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 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.
per discussion with Barry Smith
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
role
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]
object
object
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]
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.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
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]
anatomical entity
connected anatomical structure
material anatomical entity
biological entity
electron
polypeptide
hyaluronic acid
protein polypeptide chain
peptide
glycan
glycoprotein
glycosaminoglycan
acyl group
aminoglycan
carbamoyl group
molecular entity
chemical entity
group
nitrogen atom
nonmetal atom
organic sulfate
oxygen atom
oxygen molecular entity
sulfuric ester
sulfates
sulfur atom
sulfur molecular entity
univalent carboacyl group
carbon atom
amide
fundamental particle
oxoacid derivative
organic group
atom
atomic nucleus
nucleon
primary amide
heteroorganic entity
pnictogen
pnictogen molecular entity
chalcogen
chalcogen molecular entity
carbon group element atom
main group element atom
sulfur oxoacid derivative
p-block element atom
main group molecular entity
carbon group molecular entity
p-block molecular entity
biomacromolecule
information biomacromolecule
proteinogenic amino-acid residue
amino-acid residue
alpha-amino-acid residue
conjugated protein
macromolecule
organonitrogen compound
ester
sulfated glycosaminoglycan
carbohydrate sulfate
protein
lepton
baryon
fermion
subatomic particle
composite particle
hadron
nuclear particle
polyatomic entity
organochalcogen compound
organooxygen compound
mucopolysaccharide
heteroatomic molecular entity
carboxamide
sulfuric acid derivative
carboacyl group
mineral
phosphate mineral
organic amino compound
organic molecular entity
nitrogen molecular entity
apatite
hydroxylapatite
chemical substance
carbohydrate derivative
polysaccharide derivative
exopolysaccharide
carbohydrates and carbohydrate derivatives
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CALOHA:TS-2035
FMA:68646
GO:0005623
KUPO:0000002
VHOG:0001533
WBbt:0004017
XAO:0003012
cell
CL:0000000
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
cell
cell
A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
CARO:0000013
cell in vivo
cell
CL:0000003
To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).
native cell
Any fibroblast that is deriived from the neural crest.
cell
CL:0000005
fibroblast neural crest derived
neuronal receptor cell (sensu Animalia)
cell
CL:0000006
neuronal receptor cell
A cell found in the embryo before the formation of all the gem layers is complete.
cell
CL:0000007
early embryonic cell (metazoa)
Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination.
cell
CL:0000008
migratory cranial neural crest cell
Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination.
cell
CL:0000011
migratory trunk neural crest cell
Male germ cell is a germ cell that supports male gamete production.
FMA:72290
MA:0002765
VHOG:0001531
ncithesaurus:Spermatogenic_Cell
cell
CL:0000015
male germ cell
A male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids.
BTO:0001275
CALOHA:TS-0951
EMAPA:31484
FBbt:00004936
FMA:84049
WBbt:0006799
cell
CL:0000017
spermatocyte
A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa.
BTO:0001274
CALOHA:TS-0950
EMAPA:31486
FBbt:00004942
FMA:72294
WBbt:0006800
nematoblast
cell
CL:0000018
spermatid
A mature male germ cell that develops from a spermatid.
BTO:0001277
BTO:0002046
CALOHA:TS-0949
FBbt:00004954
FMA:67338
WBbt:0006798
sperm cell
spermatozoid
spermatozoon
cell
CL:0000019
sperm
An euploid male germ cell of an early stage of spermatogenesis.
BTO:0000958
CALOHA:TS-2193
EMAPA:31482
FBbt:00004935
FMA:72291
cell
CL:0000020
spermatogonium
Female germ cell is a germ cell that supports female gamete production.
MA:0000388
VHOG:0001530
ncithesaurus:Egg
cell
CL:0000021
female germ cell
A female germ cell that has entered meiosis.
BTO:0000964
CALOHA:TS-0711
FBbt:00004886
FMA:18644
WBbt:0006797
cell
oogonium
CL:0000023
oocyte
A smooth muscle cell derived from the neural crest.
cell
CL:0000027
smooth muscle cell neural crest derived
cell
CL:0000029
neuron neural crest derived
FBbt:00005145
cell
CL:0000030
glioblast
A cell that will develop into a neuron often after a migration phase.
CL:0000337
BTO:0000930
FMA:70563
neuroblast
cell
CL:0000031
neuroblast (sensu Vertebrata)
A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
CALOHA:TS-2086
FMA:63368
cell
CL:0000034
stem cell
A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119.
BTO:0000725
CALOHA:TS-0448
FMA:70337
FMA:86475
VHOG:0001485
HSC
blood forming stem cell
hemopoietic stem cell
cell
colony forming unit hematopoietic
CL:0000037
Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative.
hematopoietic stem cell
A progenitor cell committed to the erythroid lineage.
BTO:0004911
cell
BFU-E
CFU-E
blast forming unit erythroid
burst forming unit erythroid
colony forming unit erythroid
erythroid stem cell
CL:0000038
erythroid progenitor cell
A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring.
cell
CL:0000039
Originally this term had some plant germ line cell children.
germ line cell
A stem cell that can give rise to multiple lineages of cells.
FMA:84789
multi-fate stem cell
multifate stem cell
multipotent cell
multipotent stem cell
cell
CL:0000048
multi fate stem cell
A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages.
BTO:0004730
CMP
common myeloid precursor
cell
CFU-GEMM
CFU-S
colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte
multipotential myeloid stem cell
myeloid stem cell
pluripotent stem cell (bone marrow)
CL:0000049
This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059).
common myeloid progenitor
A progenitor cell committed to the megakaryocyte and erythroid lineages.
CFU-EM
CFU-MegE
MEP
Meg/E progenitor
colony forming unit erythroid megakaryocyte
megakaryocyte/erythrocyte progenitor
megakaryocyte/erythroid progenitor cell
cell
CL:0000050
MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2.
megakaryocyte-erythroid progenitor cell
A stem cell from which all cells of the body can form.
FMA:84790
totipotential stem cell
cell
CL:0000052
totipotent stem cell
A precursor cell with a limited number of potential fates.
BTO:0000125
FMA:84782
blast cell
cell
CL:0000055
define using PATO mulit-potent or oligopotent?
non-terminally differentiated cell
A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.
BTO:0000222
CALOHA:TS-0650
FBbt:00005083
FMA:70335
VHOG:0001529
cell
CL:0000056
myoblast
A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.
BTO:0000452
CALOHA:TS-0362
FMA:63877
VHOG:0001482
cell
CL:0000057
These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative.
fibroblast
Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell.
BTO:0003607
FMA:66783
chrondoplast
cell
CL:0000058
chondroblast
Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell.
BTO:0001769
CALOHA:TS-0696
FMA:62999
cell
CL:0000060
legacy def: One of the cells forming the outer surface of dental pulp that produces tooth dentin.
odontoblast
A cell that has a filiform extrusion of the cell surface.
VHOG:0001532
XAO:0000031
cell
CL:0000064
ciliated cell
A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
BTO:0000414
CALOHA:TS-2026
CARO:0000077
FBbt:00000124
FMA:66768
WBbt:0003672
epitheliocyte
cell
CL:0000066
epithelial cell
An epithelial cell that has a cilia.
FMA:70605
cell
CL:0000067
ciliated epithelial cell
An epithelial cell that is part of a duct.
cell
CL:0000068
duct epithelial cell
An endothelial cell that lines the vasculature.
cuboidal endothelial cell of vascular tree
cell
CL:0000071
blood vessel endothelial cell
A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.
cell
CL:0000075
columnar/cuboidal epithelial cell
CALOHA:TS-1249
cell
CL:0000076
squamous epithelial cell
A flattened epithelial cell of mesenchymal origin that lines the serous cavity.
FMA:66773
mesotheliocyte
cell
CL:0000077
mesothelial cell
A cell found predominately in the blood.
FMA:62844
cell
CL:0000081
blood cell
cell
CL:0000095
neuron associated cell
A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells.
neuroepithelial cell
BTO:0004301
cell
CL:0000098
The term "neuroepithelial cell" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710).
sensory epithelial cell
Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions.
BTO:0003811
FBbt:00005125
FMA:67313
WBbt:0005113
cell
CL:0000099
interneuron
An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement.
BTO:0000312
FMA:83617
WBbt:0005409
motoneuron
cell
CL:0000100
motor neuron
Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
BTO:0001037
FBbt:00005124
FMA:84649
WBbt:0005759
cell
CL:0000101
sensory neuron
An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm.
BTO:0001176
CALOHA:TS-0278
FMA:66772
endotheliocyte
cell
CL:0000115
From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard].
endothelial cell
cell
CL:0000117
CNS neuron (sensu Vertebrata)
A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.
BTO:0002606
CALOHA:TS-0415
FMA:54536
neuroglial cell
cell
neuroglia
CL:0000125
glial cell
Ectoderm destined to be nervous tissue.
neurectoderm cell
cell
CL:0000133
neurectodermal cell
A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs.
CL:0002452
BTO:0002625
BTO:0003298
FMA:70546
BMSC
bone marrow stromal cells
colony-forming unit-fibroblast
marrow stromal cells
cell
CFU-F
MSC
mesenchymal precursor cell
mesenchymal progenitor cells
mesenchymal stem cell
mesenchymal stromal cell
mesenchymal stromal cells
stem cells, mesenchymal
CL:0000134
Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2.
mesenchymal stem cell
https://github.com/obophenotype/cell-ontology/issues/474
A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides.
CL:0000450
BTO:0000443
CALOHA:TS-0012
FMA:63880
adipocyte
adipose cell
cell
CL:0000136
fat cell
Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell.
BTO:0000249
CALOHA:TS-0138
FMA:66782
cartilage cell
cell
CL:0000138
chondrocyte
A pigment cell is a cell that contains pigment granules.
VHOG:0001678
chromatocyte
chromatophore
cell
CL:0000147
pigment cell
pigment cell
cell
CL:0000149
visual pigment cell
A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules.
CALOHA:TS-2085
FMA:86494
cell
CL:0000150
glandular epithelial cell
A cell that specializes in controlled release of one or more substances.
BTO:0003659
FMA:86916
cell
CL:0000151
secretory cell
A cell that secretes glycosaminoglycans.
GAG secreting cell
hyaluronic acid secreting cell
cell
CL:0000153
glycosaminoglycan secreting cell
cell
CL:0000154
protein secreting cell
cell
CL:0000159
seromucus secreting cell
A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions.
FMA:83809
endocrinocyte
cell
CL:0000163
endocrine cell
An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas.
BTO:0003865
FMA:62930
cell
CL:0000164
enteroendocrine cell
cell
CL:0000167
peptide hormone secreting cell
A cell that secretes glucagon.
FMA:84045
glucagon-secreting cell
cell
CL:0000170
glucagon secreting cell
cell
CL:0000172
somatostatin secreting cell
cell
CL:0000174
steroid hormone secreting cell
A cell whose primary function is to shorten.
cell
CL:0000183
contractile cell
A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
BTO:0000888
BTO:0000902
CALOHA:TS-2032
FBbt:00005074
FMA:67328
WBbt:0003675
muscle fiber
myocyte
cell
CL:0000187
muscle cell
A somatic cell located in skeletal muscle.
BTO:0004392
CALOHA:TS-2158
FMA:9727
skeletal muscle cell
cell
CL:0000188
cell of skeletal muscle
A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).
CL:0000191
BTO:0004576
CALOHA:TS-2159
FMA:14072
SMCs
myocytes, smooth muscle
smooth muscle fiber
non-striated muscle cell
cell
CL:0000192
smooth muscle cell
A cell that is capable of detection of a stimulus involved in sensory perception.
receptor cell
cell
CL:0000197
sensory receptor cell
A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood.
cell
CL:0000206
chemoreceptor cell
BTO:0004185
FMA:67860
Wikipedia:Olfactory_receptor_neuron
Schultze's cell
odorant receptor cell
olfactory receptor neuron
olfactory sensory neuron
cell
CL:0000207
olfactory receptor cell
A cell type found in the spherical or ovoid clusters of receptor cells found mainly in the epithelium of the tongue and constituting the end organs of the sense of taste.
FMA:67910
taste bud cell
cell
CL:0000209
taste receptor cell
A cell specialized to detect and transduce light.
BTO:0001060
CALOHA:TS-0868
FBbt:00004211
FMA:86740
cell
CL:0000210
photoreceptor cell
A cell whose function is determined by the generation or the reception of an electric signal.
cell
CL:0000211
electrically active cell
A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism.
boundary cell
cell
CL:0000213
lining cell
A meso-epithelial cell that lies between the cartilaginous fibers in the synovial membrane of a joint and produces hyaluronic acid.
BTO:0003652
CALOHA:TS-0995
FMA:66786
synoviocyte
hyaluronic acid secreting cell
cell
CL:0000214
synovial cell
A cell whose primary function is to prevent the transport of stuff across compartments.
cell
CL:0000215
barrier cell
A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier.
BTO:0001238
CALOHA:TS-0922
FMA:72298
VHOG:0001348
cell
CL:0000216
Sertoli cell
A cell that moves by its own activities.
cell
CL:0000219
motile cell
A cell of the outer of the three germ layers of the embryo.
FMA:72549
ectoderm cell
cell
CL:0000221
ectodermal cell
A cell of the middle germ layer of the embryo.
FMA:72554
mesoblast
mesoderm cell
cell
CL:0000222
mesodermal cell
A cell of the inner of the three germ layers of the embryo.
FMA:72555
endoderm cell
cell
CL:0000223
endodermal cell
A cell with more than one nucleus.
AEO:0000203
WBbt:0008074
syncitium
syncytial cell
syncytium
cell
CL:0000228
multinucleate cell
A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
BTO:0000424
CALOHA:TS-0290
FMA:81100
RBC
red blood cell
cell
CL:0000232
erythrocyte
cell
CL:0000255
eukaryotic cell
cell
CL:0000287
eye photoreceptor cell
A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism.
cell
CL:0000293
structural cell
A mature sexual reproductive cell having a single set of unpaired chromosomes.
CALOHA:TS-0395
FBbt:00005412
FMA:18649
haploid nucleated cell
cell
haploid germ cell
CL:0000300
gamete
Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid.
BTO:0003687
FMA:62511
serous cell
cell
CL:0000313
serous secreting cell
BTO:0003689
mucous cell
cell
CL:0000319
mucus secreting cell
A cell that is specialised to accumulate a particular substance(s).
cell
CL:0000325
stuff accumulating cell
cell
CL:0000327
extracellular matrix secreting cell
cell
CL:0000329
oxygen accumulating cell
A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.
FMA:86667
cell
CL:0000333
migratory neural crest cell
A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors.
cell
CL:0000335
mesenchyme condensation cell
A cell of the sclera of the eye.
cell
CL:0000347
scleral cell
cell
CL:0000349
extraembryonic cell
A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface.
FMA:83028
trophoblastic cell
cell
CL:0000351
trophoblast cell
A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.
cell
CL:0000352
epiblast cell
An undifferentiated cell produced by early cleavages of the fertilized egg (zygote).
BTO:0001473
FMA:72551
blastomere
cell
CL:0000353
blastoderm cell
A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell.
FMA:86767
cell
CL:0000355
Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo.
multi-potent skeletal muscle stem cell
An epithelial cell of the integument (the outer layer of an organism).
CL:1000396
BTO:0001470
CALOHA:TS-0283
FMA:62411
cell of epidermis
epithelial cell of skin
cell
CL:0000362
epidermal cell
Diploid cell produced by the fusion of sperm cell nucleus and egg cell.
zygote
BTO:0000854
EHDAA2:0004546
FMA:72395
cell
CL:0000365
animal zygote
A cell whose function is determined by its response to an electric signal.
cell
CL:0000393
electrically responsive cell
cell
CL:0000402
CNS interneuron
A cell that initiates an electrical signal and passes that signal to another cell.
cell
CL:0000404
electrically signaling cell
BTO:0001277
CALOHA:TS-0949
cell
CL:0000408
male gamete
A cell whose nucleus contains a single haploid genome.
cell
CL:0000413
haploid cell
cell
CL:0000447
carbohydrate secreting cell
A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere.
BTO:0002064
FMA:83624
cell
CL:0000499
stromal cell
A peptide hormone secreting cell that secretes androgen binding protein.
cell
CL:0000511
androgen binding protein secreting cell
A precursor cell destined to differentiate into cardiac muscle cell.
CL:0000714
FMA:84797
cardiac muscle progenitor cell
cardiomyocyte progenitor cell
cell
CL:0000513
cardiac muscle myoblast
A precursor cell destined to differentiate into smooth muscle myocytes.
FMA:84798
myoblast, smooth muscle
cell
satellite cell
CL:0000514
smooth muscle myoblast
A myoblast that differentiates into skeletal muscle fibers.
FMA:84799
skeletal myoblast
cell
CL:0000515
skeletal muscle myoblast
A neuron which conveys sensory information centrally from the periphery.
FMA:87653
input neuron
cell
CL:0000526
afferent neuron
A neuron which sends impulses peripherally to activate muscles or secretory cells.
output neuron
cell
CL:0000527
efferent neuron
cell
CL:0000530
primary neuron
cell
CL:0000531
primary sensory neuron
The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
BTO:0000938
CALOHA:TS-0683
FBbt:00005106
FMA:54527
VHOG:0001483
WBbt:0003679
nerve cell
cell
CL:0000540
These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.
neuron
neuron
An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.
FMA:83518
rubriblast
cell
pronormoblast
CL:0000547
proerythroblast
cell
CL:0000548
animal cell
A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.
FMA:83505
basophilic normoblast
early erythroblast
early normoblast
prorubricyte
cell
CL:0000549
basophilic erythroblast
A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.
FMA:83506
intermediate erythroblast
intermediate normoblast
polychromatic erythroblast
polychromatic normoblast
polychromatophilic normoblast
rubricyte
cell
CL:0000550
polychromatophilic erythroblast
The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated.
FMA:84646
acidophilic erythroblast
eosinophilic erythroblast
late erythoblast
orthochromatic normoblast
pyknotic eto enrythroblast
cell
CL:0000552
orthochromatic erythroblast
An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.
BTO:0001173
CALOHA:TS-0864
cell
CL:0000558
reticulocyte
A mesenchymal stem cell capable of developing into blood vessel endothelium.
angioblast
chondroplast
cell
CL:0000566
These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive.
angioblastic mesenchymal cell
One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision.
BTO:0001036
CALOHA:TS-0866
FMA:67748
cell
CL:0000573
retinal cone cell
The reproductive cell in multicellular organisms.
BTO:0000535
VHOG:0001534
WBbt:0006796
cell
CL:0000586
germ cell
A steroid hormone secreting cell that secretes androgen.
cell
CL:0000593
androgen secreting cell
One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision.
BTO:0001024
CALOHA:TS-0870
FMA:67747
cell
CL:0000604
retinal rod cell
A cell whose primary function is to support other cell types.
BTO:0002315
cell
CL:0000630
supportive cell
A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes.
BTO:0001115
CALOHA:TS-2194
FMA:72292
cell
CL:0000656
primary spermatocyte
One of the two haploid cells into which a primary spermatocyte divides, and which in turn gives origin to spermatids.
BTO:0000709
CALOHA:TS-2195
FBbt:00004941
FMA:72293
cell
CL:0000657
secondary spermatocyte
An extracellular matrix secreting cell that secretes collagen.
cell
CL:0000667
collagen secreting cell
A non-terminally differentiated cell that is capable of developing into a muscle cell.
cell
CL:0000680
muscle precursor cell
A cell that stores and secretes pancreatic polypeptide hormone.
FMA:62938
FMA:83409
type F enteroendocrine cell
cell
CL:0000696
PP cell
Epithelial cells derived from neural plate and neural crest.
neuroepithelial cell
BTO:0004301
FMA:70557
cell
CL:0000710
The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098).
neurecto-epithelial cell
A stem cell that can give rise to cell types of the body other than those of the germ-line.
CALOHA:TS-2086
FMA:63368
cell
CL:0000723
somatic stem cell
Muscle cell which has as its direct parts myofilaments organized into sarcomeres.
BTO:0002916
CALOHA:TS-2157
FMA:86936
cell
CL:0000737
striated muscle cell
The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve.
BTO:0001800
FMA:67765
RGC
gangliocyte
ganglion cell of retina
cell
CL:0000740
retinal ganglion cell
Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei.
FMA:83808
cardiocyte
BTO:0001539
CALOHA:TS-0115
FMA:14067
cardiac muscle fiber
cardiac myocyte
cardiomyocyte
heart muscle cell
cell
CL:0000746
This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction.
cardiac muscle cell
A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
BTO:0001441
CALOHA:TS-0647
cell
CL:0000763
myeloid cell
A immature or mature cell in the lineage leading to and including erythrocytes.
CL:0002156
CALOHA:TS-0290
FMA:62845
FMA:83516
erythropoietic cell
cell
CL:0000764
Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes.
erythroid lineage cell
A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.
BTO:0001571
CALOHA:TS-0289
FMA:83504
normoblast
cell
CL:0000765
erythroblast
A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans.
BTO:0000725
CALOHA:TS-0448
MPP
hemopoietic progenitor cell
cell
CL:0000837
Markers differ between mouse and human.
hematopoietic multipotent progenitor cell
A progenitor cell restricted to the myeloid lineage.
myeloid progenitor cell
BTO:0004730
CALOHA:TS-2099
FMA:70339
cell
CL:0000839
Note that this is a class of cell types, not an identified single cell type.
myeloid lineage restricted progenitor cell
A cell of a hematopoietic lineage.
BTO:0000574
CALOHA:TS-2017
FMA:70366
FMA:83598
haematopoietic cell
haemopoietic cell
hemopoietic cell
cell
CL:0000988
hematopoietic cell
A connective tissue cell found in bone.
adiehl
2011-11-16T04:28:16Z
cell
CL:0001035
bone cell
A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells.
tmeehan
2010-01-06T03:43:20Z
cell
CL:0002031
hematopoietic lineage restricted progenitor cell
A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities.
tmeehan
2010-01-06T03:43:27Z
cell
CL:0002032
This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060).
hematopoietic oligopotent progenitor cell
An enteroendocrine cell that produces glucagon.
tmeehan
2010-09-10T10:48:54Z
FMA:62939
cell
CL:0002067
type A enteroendocrine cell
Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter.
tmeehan
2010-06-28T08:36:15Z
BTO:0001032
FMA:14146
Purkinje cell fiber
Purkinje muscle cell
myocytus conducens cardiacus
cell
CL:0002068
Purkinje myocyte
A specialized cardiac myocyte in the sinoatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery.
tmeehan
2010-06-29T11:41:37Z
pacemaker cell
BTO:0004190
FMA:67101
P cell
cardiac pacemaker cell
myocytus nodalis
cell
CL:0002072
nodal myocyte
Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes.
tmeehan
2010-06-29T02:39:32Z
FMA:67142
cell
CL:0002073
transitional myocyte
The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides).
tmeehan
2010-06-29T11:50:47Z
FMA:67111
cell
CL:0002074
myocardial endocrine cell
An epithelial cell derived from endoderm.
tmeehan
2010-06-29T03:38:14Z
FMA:69075
cell
CL:0002076
endo-epithelial cell
An epithelial cell derived from ectoderm.
tmeehan
2010-06-29T03:38:22Z
FMA:69074
cell
CL:0002077
ecto-epithelial cell
Epithelial cell derived from mesoderm or mesenchyme.
tmeehan
2010-06-29T03:49:14Z
FMA:69076
epithelial mesenchymal cell
cell
CL:0002078
meso-epithelial cell
A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart.
tmeehan
2010-07-21T01:33:38Z
FMA:67968
cell
CL:0002086
specialized cardiac myocyte
A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells.
tmeehan
2010-07-22T04:48:15Z
BTO:0004850
FMA:83621
cell
CL:0002092
MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense.
bone marrow cell
A cell in the hilum of the ovary that produces androgens.
tmeehan
2010-08-23T11:18:18Z
FMA:18710
hilar cell of ovary
cell
CL:0002095
hilus cell of ovary
A stomal cell of the ovary
tmeehan
2010-08-23T12:10:31Z
FMA:72299
ovarian stromal cell
cell
CL:0002132
stromal cell of ovary
An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels.
tmeehan
2010-08-24T02:06:40Z
BTO:0001854
CALOHA:TS-1106
FMA:67755
vascular endothelial cell
cubodial endothelial cell of vascular tree
cell
CL:0002139
These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive.
endothelial cell of vascular tree
Epithelial cells derived from general body ectoderm and ectoderm placodes.
tmeehan
2010-08-26T08:31:08Z
FMA:70556
cell
CL:0002159
general ecto-epithelial cell
A fibroblast in the bone marrow.
tmeehan
2010-09-07T02:25:18Z
FMA:84377
cell
CL:0002240
marrow fibroblast
A cell containing at least one nucleus.
tmeehan
2010-09-07T03:32:33Z
FMA:67513
cell
CL:0002242
nucleate cell
A cell that is part of the nervous system.
tmeehan
2010-09-15T01:34:57Z
CALOHA:TS-2040
FMA:70333
cell
CL:0002319
neural cell
A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.
tmeehan
2010-09-15T03:01:54Z
CL:1000406
CALOHA:TS-2096
FMA:63875
cell
CL:0002320
connective tissue cell
A cell of the embryo.
tmeehan
2010-09-15T03:39:21Z
CALOHA:TS-0263
FMA:82840
FMA:82841
WBbt:0007028
cell
CL:0002321
embryonic cell (metazoa)
A fat cell derived from a neural crest cell.
tmeehan
2010-09-20T02:25:25Z
cell
CL:0002333
neural crest derived fat cell
A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell).
tmeehan
2010-09-24T09:44:42Z
BTO:0001268
FMA:72300
WBbt:0008378
cell
CL:0002371
somatic cell
A transversely striated, synctial muscle cell, formed by the fusion of myoblasts.
tmeehan
2010-09-24T01:13:01Z
CL:0000369
myotubule
single cell sarcomere
cell
CL:0002372
myotube
A cell located in the heart, including both muscle and non muscle cells.
tmeehan
2010-12-07T09:37:22Z
BTO:0001539
CALOHA:TS-0115
FMA:83808
FMA:84791
heart cell
cell
CL:0002494
From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart.
cardiocyte
A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc
tmeehan
2010-12-07T04:03:56Z
BTO:0002441
FMA:84639
cell
CL:0002503
adventitial cell
An endothelial progenitor cell that participates in angiogenesis during development.
tmeehan
2011-02-28T04:20:39Z
cell
CL:0002546
See CL:0002619.
embryonic blood vessel endothelial progenitor cell
A cell of the seminiferous tubule epithelium.
tmeehan
2011-03-15T11:59:23Z
cell
CL:0002625
seminiferous tubule epithelial cell
A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells.
tmeehan
2011-08-16T02:38:01Z
cell
CL:0002672
retinal progenitor cell
A neuroblast derived from a neural crest cell.
tmeehan
2011-08-22T09:24:15Z
cell
CL:0002676
neural crest derived neuroblast
A CNS interneuron located in the spinal cord.
cell
CL:0005000
Is_a interneuron, part_of UBERON:0002240.
spinal cord interneuron
Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized).
haendel
2012-06-15T02:51:27Z
scleroblast
cell
CL:0007001
Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts)
skeletogenic cell
Skeletogenic cell that has the potential to form an odontoblast, deposits predentine, and arises from a cranial neural crest cell.
haendel
2012-06-15T05:15:11Z
cell
CL:0007003
preodontoblast
Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells.
haendel
2012-06-27T08:27:35Z
cell
CL:0007004
premigratory neural crest cell
Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells.
haendel
2012-06-27T10:44:01Z
cell
CL:0007009
prechondroblast
Any muscle cell in which the fibers are not organised into sarcomeres.
CL:0008000
non-striated muscle cell
Any hematopoietic cell that is a precursor of some other hematopoietic cell type.
CL:0008001
hematopoietic precursor cell
A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
CL:0008002
skeletal muscle fiber
A muscle cell that is part of some visceral muscle
CL:0008007
visceral muscle cell
A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration.
mesenchyme cell
CL:0008019
mesenchymal cell
camera type eye photoreceptor cell
CL:0010009
camera-type eye photoreceptor cell
A zygote in a plant or an animal.
CL:0010017
zygote
cell
CL:0010021
cardiac myoblast
A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.
cell
CL:0011012
neural crest cell
A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses.
http://orcid.org/0000-0001-5208-3432
CL:0011026
progenitor cell
A cell that, by division or terminal differentiation, can give rise to other cell types.
CL:0011115
Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell.
precursor cell
trophectoderm cell
cell
CL:1000274
trophectodermal cell
A fibroblast that is part of the areolar connective tissue.
FMA:261279
cell
CL:1000303
fibroblast of areolar connective tissue
A fibroblast that is part of the tunica adventitia of artery.
FMA:261285
cell
CL:1000306
fibroblast of tunica adventitia of artery
A fat cell that is part of the epicardial fat.
FMA:261293
adipocyte of epicardial fat
epicardial fat cell
cell
CL:1000309
epicardial adipocyte
A muscle cell that is part of the sinoatrial node.
FMA:67102
SA nodal myocyte
SA node cardiac muscle cell
myocyte of sinoatrial node
sinoatrial node cell
sinoatrial node myocyte
sinuatrial node myocyte
cell
CL:1000409
myocyte of sinoatrial node
A muscle cell that is part of the atrioventricular node.
FMA:67106
AV nodal myocyte
AV node cardiac muscle cell
AV node cell
atrioventricular node cell
atrioventricular node myocyte
cell
CL:1000410
myocyte of atrioventricular node
Any native cell that is part of a cardiac septum.
TermGenie
2014-06-24T23:17:07Z
cell
CL:2000022
cardiac septum cell
Any neuron that is part of a central nervous system.
TermGenie
2014-06-25T01:17:43Z
cell
CL:2000029
central nervous system neuron
biome
terrestrial biome
environmental system
ecosystem
A length measurement of the body that includes the tail.
total length
body length with tail
A length measurement of the body that includes the tail.
https://orcid.org/0000-0003-2699-3066
A length measurement of the body that excludes a tail, usually ending at the anus.
snout-vent length
head-body length
body length without tail
A length measurement of the body that excludes a tail, usually ending at the anus.
https://orcid.org/0000-0003-2699-3066
A length measurement of a hind foot that includes a nail.
pes length with claw
hind foot length with nail
A length measurement of a hind foot that includes a nail.
https://orcid.org/0000-0003-2699-3066
A length measurement of a hind foot that excludes a nail.
pes length without claw
hind foot length without nail
A length measurement of a hind foot that excludes a nail.
https://orcid.org/0000-0003-2699-3066
The length of a line of an ear from a helix of the outer ear to an intertragus insicusure of an ear.
ear length
ear notch
ear length to notch
The length of a line of an ear from a helix of the outer ear to an intertragus insicusure of an ear.
https://orcid.org/0000-0003-2699-3066
The length of a line of a femur from a medial condyle of a femur to a greater trochanter of a femur.
femur greatest length
femur length
femur length from greater trochanter to medial condyle
The length of a line of a femur from a medial condyle of a femur to a greater trochanter of a femur.
ISBN: 9004086161, 9789004086166
The length of a line of a femur from a medial condyle of a femur to a head of a femur.
femur length
femur length from caput to medial condyle
The length of a line of a femur from a medial condyle of a femur to a head of a femur.
ISBN: 9004086161, 9789004086166
The length of a line of a trochlea of a humerus to a proximal head of a humerus.
humerus length
humerus length to caput
humerus length from trochlea to caput
The length of a line of a trochlea of a humerus to a proximal head of a humerus.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The length of a line of a trochlea of a humerus to a ventral tubercle of a humerus.
humerus greatest length
humerus length
humerus length from trochlea to greater tubercle
humerus length from trochlea to ventral tubercle
The length of a line of a trochlea of a humerus to a ventral tubercle of a humerus.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
OBSOLETE Medial-lateral width of the distal end of an astragalus.
astragalus greatest breadth distal
talus distal width ML
talus head width
Redundant with FOVT:0000017
astragalus head breadth
obsolete talus distal articular breadth
true
OBSOLETE Length between the proximal-most points of the medial and lateral trochlear ridges of an astragalus.
breadth of the trochlea
breadth of the trochlea of talus
This is not a measurement FOVT has a need for.
obsolete width of the trochlea of talus
true
The length of the lateral side of a talus along the proximal-distal axis (in animals) or anterior-posterior axis (in humans).
astragalus length lateral
talus lateral length
The length of the lateral side of a talus along the proximal-distal axis (in animals) or anterior-posterior axis (in humans).
ISBN: 9780873659505
OBSOLETE The depth of the medial ridge of a trochlea of an astragalus along the anterior-posterior axis.
astragalus medial depth
astragalus medial width AP
talus medial width AP
duplicate term
obsolete talus medial depth
true
OBSOLETE Length of the lateral side of an astragalus.
Redundant term
obsolete length of the lateral side of talus
true
The length of the medial side of a talus along the proximal-distal axis (non-plantigrade) or anterior-posterior axis (plantigrade).
astragalus medial length
talus medial length
The length of the medial side of a talus along the proximal-distal axis (non-plantigrade) or anterior-posterior axis (plantigrade).
ISBN: 9780873659505
The length of a line between the medial-most point on the articular surface for the calcaneum on the astragalus to the lateral-most point of the trochleated head of an astragalus.
astragalus distal articular breadth (non-plantigrade)
astragalus distal articular width ML (non-plantigrade)
length of line between the medial-most point of the articular surface for the calcaneum on the talus to the lateral-most point of the trochleated head on talus
talus anterior articular breadth (plantigrade)
talus anterior articular width ML (plantigrade)
talus distal articular width ML (non-plantigrade)
talus distal articular breadth (non-plantigrade)
The length of a line between the medial-most point on the articular surface for the calcaneum on the astragalus to the lateral-most point of the trochleated head of an astragalus.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
Length of the distal end of an astragalus along the anterior-posterior axis (non-plantigrade) or proximal-distal axis (plantigrade).
astragalus distal articular depth (non-plantigrade)
astragalus distal articular width AP (non-plantigrade)
length of line connecting the posterior-most point ot the anterior-most point of the trochleated head on talus
talus anterior articular depth (plantigrade)
talus anterior articular width PD (plantigrade)
talus distal articular width AP (non-plantigrade)
talus distal articular depth (non-plantigrade)
Length of the distal end of an astragalus along the anterior-posterior axis (non-plantigrade) or proximal-distal axis (plantigrade).
ISBN: 9004086161, 9789004086166
The length of a talus along the proximal-distal axis (non-plantigrade) or anterior-posterior axis (plantigrade).
astragulus length
talus height
some 'Artiodactyla'
talus length
The length of a talus along the proximal-distal axis (non-plantigrade) or anterior-posterior axis (plantigrade).
ISBN: 9780873659505
talus height
von den Driesch, Angela. A guide to the measurement of animal bones from archaeological sites: as developed by the Institut für Palaeoanatomie, Domestikationsforschung und Geschichte der Tiermedizin of the University of Munich . Vol. 1. Peabody Museum Press, 1976.
The width of a talus along the medial-lateral axis.
astragalus breadth
astragalus width ML
talus width ML
talus breadth
The width of a talus along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The maximal length of a calcaneus along the proximal-distal axis (non-plantigrade) or anterior-posterior axis (plantigrade).
calcaneus length
The maximal length of a calcaneus along the proximal-distal axis (non-plantigrade) or anterior-posterior axis (plantigrade).
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width of a caclcaneus along the medial-lateral axis of the distal end (non-plantigrade) or anterior end (plantigrade).
calcaneus anterior breadth (plantigrade)
calcaneus anterior width ML (plantigrade)
calcaneus distal width ML (non-plantigrade)
calcaneus distal breadth (non-plantigrade)
The width of a caclcaneus along the medial-lateral axis of the distal end (non-plantigrade) or anterior end (plantigrade).
ISBN: 9004086161, 9789004086166
The length of a tibia on the lateral side of a tibia along the proximal-distal axis (in animals) or anterior-posterior axis (in humans).
tibia lateral length
The length of a tibia on the lateral side of a tibia along the proximal-distal axis (in animals) or anterior-posterior axis (in humans).
ISBN: 9780873659505
The width of shaft or diaphysis of a tibia.
tibia width
tibia diaphysis width
The width of shaft or diaphysis of a tibia.
https://orcid.org/0000-0003-2699-3066
The width of the proximal end of a tibia.
breadth of proximal end of tibia
tibia proximal width
The width of the proximal end of a tibia.
https://orcid.org/0000-0003-2699-3066
The width of the distal end of a tibia.
breadth of distal end of tibia
tibia distal width
The width of the distal end of a tibia.
https://orcid.org/0000-0003-2699-3066
OBSOLETE The depth of the distal end of a tibia.
tibia distal width ML
duplicate term
obsolete tibia distal breadth
true
The length of a tooth row.
tooth row length
The length of a tooth row.
https://orcid.org/0000-0003-2699-3066
Body length measured from tip of nose to cloaca.
head-body length
snout-vent length
Body length measured from tip of nose to cloaca.
https://orcid.org/0000-0003-2699-3066
The length of a line of an ear from a helix of the outer ear to a tragus of an ear. This measurement is often taken in bats.
2021-01-26T21:39:38Z
ear length to tragus
The length of a line of an ear from a helix of the outer ear to a tragus of an ear. This measurement is often taken in bats.
https://orcid.org/0000-0003-2699-3066
The width of a tibia at the distal end along the medial-lateral axis.
2021-02-05T00:08:49Z
tibia distal width ML
tibia distal breadth
The width of a tibia at the distal end along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width of a tibia at the distal end along the anterior-posterior axis (in animals) or proximal-distal axis (in humans).
2021-02-05T00:09:47Z
tibia distal width AP
some 'Equide'
some 'Lagomorpha'
tibia distal depth
The width of a tibia at the distal end along the anterior-posterior axis (in animals) or proximal-distal axis (in humans).
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width of a tibia at the proximal end along the medial-lateral axis.
2021-02-05T00:10:13Z
tibia proximal width ML
tibia proximal breadth
The width of a tibia at the proximal end along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width of a tibia at the proximal end along the anterior-posterior axis (in animals) or proximal-distal axis (in humans).
2021-02-05T00:10:31Z
tibia proximal width AP
tibia proximal depth
The width of a tibia at the proximal end along the anterior-posterior axis (in animals) or proximal-distal axis (in humans).
ISBN: 9004086161, 9789004086166
https://eprints.nottingham.ac.uk/50198/
The width of a shaft or diaphysis of a tibia along the medial-lateral axis.
2021-02-05T00:16:17Z
tibia diaphysis width ML
tibia diaphysis breadth
The width of a shaft or diaphysis of a tibia along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width of a shaft or diaphysis of a tibia along the anterior-posterior axis (in animals) or proximal-distal axis (in humans).
2021-02-05T00:16:59Z
tibia diaphysis width AP
tibia diaphysis depth
The width of a shaft or diaphysis of a tibia along the anterior-posterior axis (in animals) or proximal-distal axis (in humans).
ISBN: 9004086161, 9789004086166
The length of a tibia on the medial side along the proximal-distal axis (in animals) or anterior-posterior axis (in humans).
2021-02-10T21:45:47Z
tibia medial length
The length of a tibia on the medial side along the proximal-distal axis (in animals) or anterior-posterior axis (in humans).
ISBN: 9004086161, 9789004086166
OBSOLETE The greatest length of a tibia from the proximal-most point of a tibia to the distal-most point of a tibia.
2021-02-10T21:53:59Z
duplicate of a term in OBA
obsolete tibia greatest length
true
OBSOLETE The greatest length of a tibia from the proximal-most point of a tibia to the distal-most point of a tibia.
Eisenmann, Véra, and V. Eisenmann Michael O. Woodburne PY. Studying Fossil Horses: Collected Papers After the New York International Hipparion Conference, 1981. Vol. 1. Brill Archive, 1988.
von den Driesch, Angela. A guide to the measurement of animal bones from archaeological sites: as developed by the Institut für Palaeoanatomie, Domestikationsforschung und Geschichte der Tiermedizin of the University of Munich . Vol. 1. Peabody Museum Press, 1976.
The circumference of the diaphysis of a tibia.
2021-02-10T21:58:04Z
tibia diaphysis circumference
The circumference of the diaphysis of a tibia.
ISBN: 9780873659505
The width of the proximal end of a femur along the medial-lateral axis.
2021-02-10T22:28:39Z
femur proximal width ML
femur proximal breadth
The width of the proximal end of a femur along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width of the trochanter of a femur along the medial-lateral axis.
2021-02-10T22:32:15Z
femur trochanter width ML
femur trochanter breadth
The width of the trochanter of a femur along the medial-lateral axis.
ISBN: 9780873659505
The width of the caput of a femur along the anterior-posterior axis.
2021-02-10T22:33:22Z
femur caput width AP
femur caput depth
The width of the caput of a femur along the anterior-posterior axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width of the diaphysis of a femur along the medial-lateral axis.
2021-02-10T22:35:17Z
femur diaphysis width ML
femur diaphysis breadth
The width of the diaphysis of a femur along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The circumference of the diaphysis of a femur.
2021-02-10T22:36:50Z
femur diaphysis circumference
The circumference of the diaphysis of a femur.
ISBN: 9780873659505
The width of the distal end of a femur along the medial-lateral axis.
2021-02-10T22:37:49Z
femur distal width ML
femur distal breadth
The width of the distal end of a femur along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width of the proximal end of a femur along the anterior-posterior axis.
2021-02-10T22:44:52Z
femur proximal width AP
femur proximal depth
The width of the proximal end of a femur along the anterior-posterior axis.
ISBN: 9004086161, 9789004086166
The width of the distal end of a femur along the anterior-posterior axis.
2021-02-10T22:46:33Z
femur distal width AP
femur distal depth
The width of the distal end of a femur along the anterior-posterior axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
femur distal width AP
Eisenmann, Véra, and V. Eisenmann Michael O. Woodburne PY. Studying Fossil Horses: Collected Papers After the New York International Hipparion Conference, 1981. Vol. 1. Brill Archive, 1988.
The width of the trochlea of a femur along the medial-lateral axis.
2021-02-10T22:47:31Z
femur trochlea width ML
femur trochlea breadth
The width of the trochlea of a femur along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
The width of the diaphysis of a femur along the anterior-posterior axis.
2021-02-10T22:52:48Z
femur diaphysis width AP
femur diaphysis depth
The width of the diaphysis of a femur along the anterior-posterior axis.
ISBN: 9004086161, 9789004086166
The width of the diaphysis of a humerus along the medial-lateral axis.
2021-02-10T22:56:30Z
humerus diaphysis width ML
humerus diaphysis breadth
The width of the diaphysis of a humerus along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
https://doi.org/10.1111/j.1096-3642.1983.tb00098.x
The width of the proximal end of a humerus along the medial-lateral axis.
Canidae
Lagomorpha
2021-02-10T22:57:22Z
humerus proximal width ML
humerus proximal breadth
The width of the proximal end of a humerus along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width of the trochlea of a humerus along the medial-lateral axis.
2021-02-10T23:01:47Z
humerus trochlea width ML
Equidae
Ruminantia
humerus trochlea breadth
The width of the trochlea of a humerus along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
https://doi.org/10.1111/j.1096-3642.1983.tb00098.x
The width of the distal end of a humerus along the anterior-posterior axis.
2021-02-10T23:02:42Z
humerus distal width AP
humerus distal depth
The width of the distal end of a humerus along the anterior-posterior axis.
ISBN: 9004086161, 9789004086166
The width of the proximal end of a humerus along the anterior-posterior axis.
2021-02-10T23:04:06Z
humerus proximal width AP
Canidae
Lagomorpha
humerus proximal depth
The width of the proximal end of a humerus along the anterior-posterior axis.
ISBN: 9780873659505
The width of the distal end of a humerus along the medial-lateral axis.
2021-02-10T23:05:13Z
humerus distal width ML
humerus distal breadth
The width of the distal end of a humerus along the medial-lateral axis.
ISBN: 9780873659505
The width of the diaphysis of a humerus along the anterior-posterior axis.
2021-02-10T23:06:16Z
humerus diaphysis width AP
humerus diaphysis depth
The width of the diaphysis of a humerus along the anterior-posterior axis.
https://doi.org/10.1111/j.1096-3642.1983.tb00098.x
The width of a talus.
2021-02-10T23:12:24Z
astragalus width
talus width
The width of a talus.
https://orcid.org/0000-0003-2699-3066
The width of the lateral side of a talus along the anterior-posterior axis ( non-plantigrade) or proximal-distal axis (plantigrade).
2021-02-10T23:16:34Z
astragalus lateral depth
astragalus lateral width AP (non-plantigrade)
talus lateral width AP (non-plantigrade)
talus lateral width PD (plantigrade)
talus lateral depth
The width of the lateral side of a talus along the anterior-posterior axis ( non-plantigrade) or proximal-distal axis (plantigrade).
ISBN: 9780873659505
The width of the medial side of a talus along the anterior-posterior axis (non-plantigrade) or proximal-distal axis (plantigrade).
2021-02-10T23:17:22Z
astragalus medial depth
astragalus medial width AP (non-plantigrade)
talus medial width AP (non-plantigrade)
talus medial width PD (plantigrade)
talus medial depth
The width of the medial side of a talus along the anterior-posterior axis (non-plantigrade) or proximal-distal axis (plantigrade).
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width of the distal end (non-plantigrade) or anterior end (plantigrade) of a talus along the medial-lateral axis.
2021-02-10T23:20:39Z
astragalus distal width ML (non-plantigrade)
astralagalus distal breadth (non-plantigrade)
talus anterior breadth (plantigrade)
talus anterior width ML (plantigrade)
talus distal width ML (non-plantigrade)
talus distal breadth (non-plantigrade)
The width of the distal end (non-plantigrade) or anterior end (plantigrade) of a talus along the medial-lateral axis.
ISBN: 9780873659505
The length of the trochlea tali of a talus along the proximal-distal axis (in animals) or anterior-posterior axis (in humans).
2021-02-10T23:25:15Z
trochlea tali length
The length of the trochlea tali of a talus along the proximal-distal axis (in animals) or anterior-posterior axis (in humans).
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width of the trochlea of a talus along the medial-lateral axis.
2021-02-10T23:28:01Z
astragalus trochlea breadth
astragalus trochlea width ML
talus trochlea width ML
talus trochlea breadth
The width of the trochlea of a talus along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
astragalus trochlea breadth
Eisenmann, Véra, and V. Eisenmann Michael O. Woodburne PY. Studying Fossil Horses: Collected Papers After the New York International Hipparion Conference, 1981. Vol. 1. Brill Archive, 1988.
The length of the proximal end of a calcaneus along the proximal-distal axis (non-plantigrade) or posterior end of a calcaneus along the anterior-posterior axis (plantigrade).
2021-02-10T23:31:00Z
calcaneus posterior length (plantigrade)
calcaneus proximal length (non-plantigrade)
The length of the proximal end of a calcaneus along the proximal-distal axis (non-plantigrade) or posterior end of a calcaneus along the anterior-posterior axis (plantigrade).
ISBN: 9004086161, 9789004086166
The width of the distal end of a calcaneus along the anterior-posterior axis (non-plantigrade) or anterior end along the proximal-distal axis (plantigrade)
2021-02-10T23:32:25Z
calcaneus anterior depth (plantigrade)
calcaneus anterior width PD (plantigrade)
calcaneus distal width AP (non-plantigrade)
calcaneus distal depth (non-plantigrade)
The width of the distal end of a calcaneus along the anterior-posterior axis (non-plantigrade) or anterior end along the proximal-distal axis (plantigrade)
ISBN: 9004086161, 9789004086166
The mass of a multicellur organism after removing internal organs.
2021-05-10T22:50:17Z
gutted body mass
The mass of a multicellur organism after removing internal organs.
https://orcid.org/0000-0003-2699-3066
The mass of a multicellular organism after being skinned.
2021-05-10T22:52:04Z
skinned body mass
The mass of a multicellular organism after being skinned.
https://orcid.org/0000-0003-2699-3066
The mass of a multicellur organism skeletal elements (i.e., bones) without skin, internal organs, or other soft tissue.
2021-05-10T22:52:36Z
'bone mass'
skeletal body mass
The mass of a multicellur organism skeletal elements (i.e., bones) without skin, internal organs, or other soft tissue.
https://orcid.org/0000-0003-2699-3066
The mass of a mutlicellular organism after being both gutted (i.e., internal organs removed) and skinned.
2021-05-10T22:53:18Z
gutted and skinned body mass
The mass of a mutlicellular organism after being both gutted (i.e., internal organs removed) and skinned.
https://orcid.org/0000-0003-2699-3066
2021-05-10T23:15:37Z
The length of a testis.
testis length
The length of a testis.
https://orcid.org/0000-0003-2699-3066
2021-05-10T23:16:25Z
The length of the right testis.
right testis length
The length of the right testis.
https://orcid.org/0000-0003-2699-3066
2021-05-10T23:18:15Z
The length of the left testis.
left testis length
The length of the left testis.
https://orcid.org/0000-0003-2699-3066
2021-05-10T23:18:51Z
The length of a gonad.
gonad length
The length of a gonad.
https://orcid.org/0000-0003-2699-3066
Length of the lateral side of a humerus from lateral tuberosity to lateral border of the trochlea.
2021-05-10T23:37:19Z
humerus lateral length
Length of the lateral side of a humerus from lateral tuberosity to lateral border of the trochlea.
ISBN: 9780873659505
The length of an ovary.
2021-05-17T20:08:12Z
ovary length
The length of an ovary.
https://orcid.org/0000-0003-2699-3066
The length of an ovary on the right side.
2021-05-17T20:10:16Z
right ovary length
The length of an ovary on the right side.
https://orcid.org/0000-0003-2699-3066
The length of an ovary on the left side.
2021-05-17T20:10:46Z
left ovary length
The length of an ovary on the left side.
https://orcid.org/0000-0003-2699-3066
The length along the anterior-posterior axis of the anterior tibial tuberosity (fossa digitalis).
2021-05-17T20:18:01Z
fossa digitalis length
anterior tibial tuberosity length
The length along the anterior-posterior axis of the anterior tibial tuberosity (fossa digitalis).
ISBN: 9004086161, 9789004086166
The length along the medial-lateral axis of the caput of the humerus.
2021-05-18T19:52:02Z
humerus proximal depth at median tubercle
The length along the medial-lateral axis of the caput of the humerus.
ISBN: 9004086161, 9789004086166
Length along the proximal-distal axis of the trochlear sulcus of a humerus.
2021-05-18T19:55:10Z
minimal humerus trochlear height
humerus trochlear sulcus height
Length along the proximal-distal axis of the trochlear sulcus of a humerus.
ISBN: 9004086161, 9789004086166
Length along the proximal-distal axis of the distal medial trochlea of a humerus.
2021-05-18T19:56:56Z
maximal humerus trochlear height
humerus medial trochlear height
Length along the proximal-distal axis of the distal medial trochlea of a humerus.
ISBN: 9004086161, 9789004086166
Length along the proximal-distal axis of the sagittal crest of a trochlea of a humerus.
2021-05-18T20:00:02Z
humerus trochlear height at sagittal crest
Length along the proximal-distal axis of the sagittal crest of a trochlea of a humerus.
ISBN: 9004086161, 9789004086166
The length along the anterior-posterior axis of a femur connecting the caput of a femur to the lateral condyle of a femur.
2021-05-19T01:36:28Z
femur lateral length
femur length from caput to lateral condyle
The length along the anterior-posterior axis of a femur connecting the caput of a femur to the lateral condyle of a femur.
ISBN: 9004086161, 9789004086166
The length along the proximal-distal axis of an olecranon of an ulna.
2021-05-19T23:33:50Z
olecranon length
The length along the proximal-distal axis of an olecranon of an ulna.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width of the facet for the humeral head of a radius along the medial-lateral axis.
2021-05-19T23:57:14Z
ulna facies articularis proximalis breadth
ulna coronoid process breadth
ulna coronoid process width ML
ulna proximal articula width ML
ulna proximal articular breadth
The width of the facet for the humeral head of a radius along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
2021-05-20T00:00:24Z
ulna width
ulna width
https://orcid.org/0000-0003-2699-3066
The width of an olecranon of a radius along the anterior-posterior axis.
2021-05-20T00:02:15Z
olecranon width AP
olecranon depth
The width of an olecranon of a radius along the anterior-posterior axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The length along the proximal-distal axis on the lateral side of an ulna.
2021-05-20T00:04:26Z
ulna lateral length
The length along the proximal-distal axis on the lateral side of an ulna.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width along the anterior-posterior axis of the proximal-most part of the facet that articulates with the humeral head on an ulna.
2021-05-20T00:05:42Z
ulna width AP across the process anaconaeus
ulna depth across the process anaconaeus
The width along the anterior-posterior axis of the proximal-most part of the facet that articulates with the humeral head on an ulna.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The length along the midline of a talus along the proximal-distal axis (non-plantigrade) or anterior-posterior axis (plantigrade) from the groove for a flexor hallucis longus tendon of a talus to a head of a talus.
2021-05-24T20:26:44Z
length of astragalus along the midline
length of talus along the midline
The length along the midline of a talus along the proximal-distal axis (non-plantigrade) or anterior-posterior axis (plantigrade) from the groove for a flexor hallucis longus tendon of a talus to a head of a talus.
DOI:Â 10.1007/s00267-006-0240-8
The width of a calcaneal body along the medial-lateral axis.
2021-05-24T21:22:09Z
calcaneus minimal breadth
width ML of calcaneal body
breadth of calcaneal body
The width of a calcaneal body along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
https://eprints.nottingham.ac.uk/50198/
calcaneus minimal breadth
ISBN: 9004086161, 9789004086166
The width of a calcaneus.
2021-05-24T21:26:12Z
calcaneus width
The width of a calcaneus.
https://orcid.org/0000-0003-2699-3066
The width along the medial-lateral axis of the distal (non-plantigrade) or posterior (plantigrade) end of a calcaneus.
2021-05-24T21:29:06Z
calcaneus maximal breadth
calcaneus posterior breadth (plantigrade)
calcaneus posterior width ML (plantigrade)
calcaneus proximal width ML (non-plantigrade)
calcaneus proximal breadth (non-plantigrade)
The width along the medial-lateral axis of the distal (non-plantigrade) or posterior (plantigrade) end of a calcaneus.
ISBN: 9004086161, 9789004086166
calcaneus maximal breadth
ISBN: 9004086161, 9789004086166
The with of the proximal end of a calcaneus along the anterior-posterior axis (non-plantigrade) or of the posterior end of a calcaneus along the proximal-distal axis (plantigrade).
2021-05-24T21:32:39Z
calcaneus maximal depth
calcaneus posterior depth (plantigrade)
calcaneus posterior with PD (plantigrade)
calcaneus proximal width AP (non-plantigrade)
calcaneus proximal depth (non-plantigrade)
The with of the proximal end of a calcaneus along the anterior-posterior axis (non-plantigrade) or of the posterior end of a calcaneus along the proximal-distal axis (plantigrade).
ISBN: 9004086161, 9789004086166
calcaneus maximal depth
Eisenmann, Véra, and V. Eisenmann Michael O. Woodburne PY. Studying Fossil Horses: Collected Papers After the New York International Hipparion Conference, 1981. Vol. 1. Brill Archive, 1988.
The width along the anterior-posterior axis (non-plantigrade) or proximal-distal axis (plantigrade) of a calcaneal body.
2021-05-24T21:35:37Z
width AP of calcaneal body (non-plantigrade)
width PD of calcanedal body (plantigrade)
depth of calcaneal body
The width along the anterior-posterior axis (non-plantigrade) or proximal-distal axis (plantigrade) of a calcaneal body.
ISBN: 9004086161, 9789004086166
https://eprints.nottingham.ac.uk/50198/
The length of the medial side of a radius along the proximal-distal axis.
2021-06-02T23:33:11Z
radius medial length
The length of the medial side of a radius along the proximal-distal axis.
ISBN: 9004086161, 9789004086166
The length of the lateral side of a radius.
2021-06-02T23:34:54Z
radius lateral length
The length of the lateral side of a radius.
ISBN: 9780873659505
The width along the medial-lateral axis of the diaphysis of a radius.
2021-06-02T23:36:38Z
radius diaphysis breadth
The width along the medial-lateral axis of the diaphysis of a radius.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width along the anterior-posterior axis of the diaphysis of a radius.
2021-06-02T23:39:12Z
radius diaphysis depth
The width along the anterior-posterior axis of the diaphysis of a radius.
ISBN: 9004086161, 9789004086166
The width along the medial-lateral axis of the articular surface on the proximal end of a radius that interacts with the humerus.
2021-06-02T23:40:22Z
radius facies articularis proximalis breadth
some 'Equidae'
some 'Ruminantia'
radius proximal articular breadth
The width along the medial-lateral axis of the articular surface on the proximal end of a radius that interacts with the humerus.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width along the anterior-posterior axis of the articular surface on the proximal end of a radius that interacts with a humerus.
2021-06-02T23:42:36Z
radius proximal articular depth
The width along the anterior-posterior axis of the articular surface on the proximal end of a radius that interacts with a humerus.
ISBN: 9004086161, 9789004086166
The width along the medial-lateral axis of the proximal end of a radius.
2021-06-02T23:43:56Z
radius proximal breadth
The width along the medial-lateral axis of the proximal end of a radius.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width along the medial-lateral axis of the distal end of a radius.
2021-06-02T23:45:18Z
radius facies articularis distalis breadth
some 'Equidae'
some 'Ruminantia'
radius distal articular breadth
The width along the medial-lateral axis of the distal end of a radius.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width along the anterior-posterior axis of the articular surface on the distal end of a radius that interacts with the carpals.
2021-06-02T23:48:26Z
radius distal articular depth
The width along the anterior-posterior axis of the articular surface on the distal end of a radius that interacts with the carpals.
ISBN: 9004086161, 9789004086166
The width along the medial-lateral axis of the distal end of a radius.
2021-06-02T23:50:24Z
radius distal breadth
The width along the medial-lateral axis of the distal end of a radius.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The length from the proximal articular surface to the distal articular surface of a radius.
2021-06-02T23:52:19Z
radius length from the proximal articular surface to the distal articular surface
The length from the proximal articular surface to the distal articular surface of a radius.
ISBN: 9780873659505
The circumference of the diaphysis of a radius.
2021-06-02T23:53:37Z
radius diaphysis circumference
The circumference of the diaphysis of a radius.
ISBN: 9780873659505
already in OBA
DEPRECATED metatarsal bone length
true
OBSOLETE The length of the metatarsal bone of digit 2 along the proximal-distal axis.
2021-06-03T22:41:34Z
already exists
obsolete metatarsal bone of digit 2 length
true
OBSOLETE The length of the metatarsal bone of digit 2 along the proximal-distal axis.
Eisenmann, Véra, and V. Eisenmann Michael O. Woodburne PY. Studying Fossil Horses: Collected Papers After the New York International Hipparion Conference, 1981. Vol. 1. Brill Archive, 1988.
von den Driesch, Angela. A guide to the measurement of animal bones from archaeological sites: as developed by the Institut für Palaeoanatomie, Domestikationsforschung und Geschichte der Tiermedizin of the University of Munich . Vol. 1. Peabody Museum Press, 1976.
OBSOLETE The length of a metatarsal bone of digit 3 along the proximal-distal axis.
2021-06-03T22:44:56Z
class already exists
obsolete metatarsal bone of digit 3 length
true
OBSOLETE The length of a metatarsal bone of digit 3 along the proximal-distal axis.
Eisenmann, Véra, and V. Eisenmann Michael O. Woodburne PY. Studying Fossil Horses: Collected Papers After the New York International Hipparion Conference, 1981. Vol. 1. Brill Archive, 1988.
von den Driesch, Angela. A guide to the measurement of animal bones from archaeological sites: as developed by the Institut für Palaeoanatomie, Domestikationsforschung und Geschichte der Tiermedizin of the University of Munich . Vol. 1. Peabody Museum Press, 1976.
OBSOLETE The length of the metatarsal bone of digit 4 along the proximal-distal axis.
2021-06-03T22:46:16Z
class already exists
obsolete metatarsal bone of digit 4 length
true
OBSOLETE The length of the metatarsal bone of digit 4 along the proximal-distal axis.
Eisenmann, Véra, and V. Eisenmann Michael O. Woodburne PY. Studying Fossil Horses: Collected Papers After the New York International Hipparion Conference, 1981. Vol. 1. Brill Archive, 1988.
von den Driesch, Angela. A guide to the measurement of animal bones from archaeological sites: as developed by the Institut für Palaeoanatomie, Domestikationsforschung und Geschichte der Tiermedizin of the University of Munich . Vol. 1. Peabody Museum Press, 1976.
OBSOLETE The length of a metatarsal bone of digit 5 along the proximal-distal axis.
2021-06-03T22:50:27Z
class already exists
obsolete metatarsal bone of digit 5 length
true
OBSOLETE The length of a metatarsal bone of digit 5 along the proximal-distal axis.
von den Driesch, Angela. A guide to the measurement of animal bones from archaeological sites: as developed by the Institut für Palaeoanatomie, Domestikationsforschung und Geschichte der Tiermedizin of the University of Munich . Vol. 1. Peabody Museum Press, 1976.
The length of a fused metatarsal bones 3 and 4 along the proximal-distal axis.
2021-06-03T23:03:13Z
fused metatarsal bones 3 and 4 length
The length of a fused metatarsal bones 3 and 4 along the proximal-distal axis.
ISBN: 9780873659505
The length of a metapodial bone.
2021-06-09T23:21:07Z
length of metapodial bone
metapodial bone length
The length of a metapodial bone.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The length of a metapodial bone of digit 2.
2021-06-09T23:23:45Z
length of metapodial bone of digit 2
metapodial bone of digit 2 length
The length of a metapodial bone of digit 2.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The length of fused metapodial bones 3 and 4.
2021-06-09T23:39:00Z
length of fused metapodial bones 3 and 4
fused metapodial bones 3 and 4 length
The length of fused metapodial bones 3 and 4.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The length of a metapodial bone of digit 4.
2021-06-09T23:42:17Z
length of metapodial bone of digit 4
metapodial bone of digit 4 length
The length of a metapodial bone of digit 4.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The length of a metapodial bone of digit 5.
2021-06-09T23:45:03Z
length of metapodial bone of digit 5
metapodial bone of digit 5 length
The length of a metapodial bone of digit 5.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The length of a metapodial bone of digit 3.
2021-06-09T23:47:16Z
length of metapodial bone of digit 3.
metapodial bone of digit 3 length
The length of a metapodial bone of digit 3.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width of a radius.
2021-06-17T00:51:35Z
Width of radius bone.
radius width
The width of a radius.
https://orcid.org/0000-0003-2699-3066
The width of the distal end of a radius.
2021-06-17T00:53:05Z
radius distal width
The width of the distal end of a radius.
https://orcid.org/0000-0003-2699-3066
The width of the proximal end of a radius.
2021-06-17T00:54:08Z
radius proximal width
The width of the proximal end of a radius.
https://orcid.org/0000-0003-2699-3066
The width of the arcitular surface that articulates with the humerus located on the proximal end of a radius.
2021-06-17T00:57:18Z
radius proximal articular width
The width of the arcitular surface that articulates with the humerus located on the proximal end of a radius.
https://orcid.org/0000-0003-2699-3066
OBSOLETE The length of a fibula along the proximal-distal axis.
2021-07-22T21:20:50Z
length of fibula
Already exists in OBA.
obsolete fibula length
true
OBSOLETE The length of a fibula along the proximal-distal axis.
von den Driesch, Angela. A guide to the measurement of animal bones from archaeological sites: as developed by the Institut für Palaeoanatomie, Domestikationsforschung und Geschichte der Tiermedizin of the University of Munich . Vol. 1. Peabody Museum Press, 1976.
The length of the dorsal side of a scapula along the proximal-distal axis.
2021-07-23T18:37:56Z
scapula dorsal length
The length of the dorsal side of a scapula along the proximal-distal axis.
ISBN: 9780873659505
Length of a scpular spine along the proximal-distal axis.
2021-07-23T19:17:25Z
length of scapular spine
scapula spine length
Length of a scpular spine along the proximal-distal axis.
ISBN: 9780873659505
The width of a scapular neck along the medial-lateral axis.
2021-07-23T19:28:14Z
breadth of scapula neck
scapula neck width ML
scapula neck breadth
The width of a scapular neck along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The length of the glenoid cavity (glenoid fossa) along the anterior-posterior axis.
2021-07-23T21:33:08Z
length of glenoid process
glenoid cavity length
The length of the glenoid cavity (glenoid fossa) along the anterior-posterior axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The width of the glenoid cavity (glenoid fossa) along the medial-lateral axis.
2021-07-23T21:36:30Z
breadth of glenoid cavity
glenoid cavity breadth
The width of the glenoid cavity (glenoid fossa) along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
The depth of a scapula along the anterior-posterior axis.
2021-07-23T21:40:46Z
depth of scapula
scapula depth
The depth of a scapula along the anterior-posterior axis.
ISBN: 9004086161, 9789004086166
The width of the diaphysis of a radius.
2021-07-27T23:38:42Z
radius diaphysis width
The width of the diaphysis of a radius.
ORCID: 0000-0003-2699-3066
Mass of the viscera (internal organs).
2021-07-27T23:56:39Z
viscera mass
Mass of the viscera (internal organs).
ORCID: 0000-0003-2699-3066
OBSOLETE The mass of the skin of an organism.
2021-07-27T23:59:50Z
Term already exists.
obsolete skin mass
true
OBSOLETE The mass of the skin of an organism.
ORCID: 0000-0003-2699-3066
The width of the radial condyle (styloid notch) of a radius along the medial-lateral axis.
2021-08-03T20:33:02Z
radial condyle breadth
The width of the radial condyle (styloid notch) of a radius along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
The width of the ulnar codyle (ulnar notch) of a radius along the medial-lateral axis.
2021-08-03T20:36:43Z
ulnar condyle breadth
The width of the ulnar codyle (ulnar notch) of a radius along the medial-lateral axis.
ISBN: 9004086161, 9789004086166
The length of a patella along the proximal-distal axis.
2021-08-04T00:39:28Z
length of patella
patella length
The length of a patella along the proximal-distal axis.
ISBN: 9780873659505
The width of a patella along th medial-lateral axis.
2021-08-04T00:41:17Z
patella width ML
patella breadth
The width of a patella along th medial-lateral axis.
ISBN: 9780873659505
The length along the anterior-posterior axis on the lateral edge of a scapula.
2021-08-12T16:57:17Z
scapula lateral depth
The length along the anterior-posterior axis on the lateral edge of a scapula.
ISBN: 9004086161, 9789004086166
ISBN: 9780873659505
2021-10-06T17:55:21Z
The length of the occlusal surface of a molar tooth 1 along the medial-lateral axis.
molar tooth 1 length ML
molar tooth 1 occlusal surface width
The length of the occlusal surface of a molar tooth 1 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a upper molar tooth 1 along the medial-lateral axis.
2021-10-06T17:58:27Z
upper molar tooth 1 length ML
upper molar tooth 1 occlusal surface width
The length of the occlusal surface of a upper molar tooth 1 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower molar tooth 1 along the medial-lateral axis.
2021-10-06T18:01:37Z
lower molar tooth 1 length ML
lower molar tooth 1 occlusal surface width
The length of the occlusal surface of a lower molar tooth 1 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper secondary molar tooth 1 along the medial-lateral axis.
2021-10-06T18:03:06Z
upper secondary molar tooth 1 length ML
upper secondary molar tooth 1 occlusal surface width
The length of the occlusal surface of an upper secondary molar tooth 1 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper primary molar tooth 1 along the medial-lateral axis.
2021-10-06T18:04:52Z
upper primary molar tooth 1 length ML
upper primary molar tooth 1 occlusal surface width
The length of the occlusal surface of an upper primary molar tooth 1 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower secondary molar tooth 1 along the medial-lateral axis.
2021-10-06T18:06:32Z
lower secondary molar tooth 1 length ML
lower secondary molar tooth 1 occlusal surface width
The length of the occlusal surface of a lower secondary molar tooth 1 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower primary molar tooth 1 along the medial-lateral axis.
2021-10-06T18:08:38Z
lower primary molar tooth 1 length ML
lower primary molar tooth 1 occlusal surface width
The length of the occlusal surface of a lower primary molar tooth 1 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a molar tooth 1 along the anterior-posterior axis.
2021-10-06T18:09:53Z
molar tooth 1 occlusal surface length AP
molar tooth 1 occlusal surface length
The length of the occlusal surface of a molar tooth 1 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper molar tooth 1 along the anterior-posterior axis.
2021-10-06T18:17:47Z
upper molar tooth 1 occlusal surface length AP
upper molar tooth 1 occlusal surface length
The length of the occlusal surface of an upper molar tooth 1 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of lower molar tooth 1 along the anterior-posterior axis.
2021-10-06T18:21:46Z
lower molar tooth 1 occlusal surface length AP
lower molar tooth 1 occlusal surface length
The length of the occlusal surface of lower molar tooth 1 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper secondary molar tooth 1 along the anterior-posterior axis.
2021-10-06T18:23:26Z
upper secondary molar tooth 1 occlusal surface length AP
upper secondary molar tooth 1 occlusal surface length
The length of the occlusal surface of an upper secondary molar tooth 1 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper primary molar tooth 1 along the anterior-posterior axis.
2021-10-06T18:24:48Z
upper primary molar tooth 1 occlusal surface length AP
upper primary molar tooth 1 occlusal surface length
The length of the occlusal surface of an upper primary molar tooth 1 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower secondary molar tooth 1 along the anterior-posterior axis.
2021-10-06T18:26:08Z
lower secondary molar tooth 1 occlusal surface length AP
lower secondary molar tooth 1 occlusal surface length
The length of the occlusal surface of a lower secondary molar tooth 1 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower primary molar tooth 1 along the anterior-posterior axis.
2021-10-06T18:27:20Z
lower primary molar tooth 1 occlusal surface length AP
lower primary molar tooth 1 occlusal surface length
The length of the occlusal surface of a molar tooth 2 along the medial-lateral axis.
2021-10-06T18:28:37Z
molar tooth 2 occlusal surface length ML
molar tooth 2 occlusal surface width
The length of the occlusal surface of a molar tooth 2 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper molar tooth 2 along the medial-lateral axis.
2021-10-06T18:30:15Z
upper molar tooth 2 occlusal surface length ML
upper molar tooth 2 occlusal surface width
The length of the occlusal surface of an upper molar tooth 2 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower molar tooth 2 along the medial-lateral axis.
2021-10-06T18:31:30Z
lower molar tooth 2 occlusal surface length ML
lower molar tooth 2 occlusal surface width
The length of the occlusal surface of a lower molar tooth 2 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper secondary molar tooth 2 along the medial-lateral axis.
2021-10-06T18:32:57Z
upper secondary molar tooth 2 occlusal surface length ML
upper secondary molar tooth 2 occlusal surface width
The length of the occlusal surface of an upper secondary molar tooth 2 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper primary molar tooth 2 along the medial-lateral axis.
2021-10-06T18:34:29Z
upper secondary molar tooth 2 occlusal surface length ML
upper primary molar tooth 2 occlusal surface width
The length of the occlusal surface of an upper primary molar tooth 2 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower secondary molar tooth 2 along the medial-lateral axis.
2021-10-06T18:35:47Z
lower secondary molar tooth 2 occlusal surface length ML
lower secondary molar tooth 2 occlusal surface width
The length of the occlusal surface of a lower secondary molar tooth 2 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower primary molar tooth 2 along the medial-lateral axis.
2021-10-06T18:37:05Z
lower primary molar tooth 2 occlusal surface length ML
lower primary molar tooth 2 occlusal surface width
The length of the occlusal surface of a lower primary molar tooth 2 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface a molar tooth 2 along the anterior-posterior axis.
2021-10-06T18:38:13Z
molar tooth 2 occlusal surface length AP
molar tooth 2 occlusal surface length
The length of the occlusal surface a molar tooth 2 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper molar tooth 2 along the anterior-posterior axis.
2021-10-06T18:39:27Z
upper molar tooth 2 occlusal surface length AP
upper molar tooth 2 occlusal surface length
The length of the occlusal surface of an upper molar tooth 2 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower molar tooth 2 along the anterior-posterior axis.
2021-10-06T18:40:48Z
lower molar tooth 2 occlusal surface length AP
lower molar tooth 2 occlusal surface length
The length of the occlusal surface of a lower molar tooth 2 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper secondary molar tooth 2 along the anterior-posterior axis.
2021-10-06T18:42:05Z
upper secondary molar tooth 2 occlusal surface length AP
upper secondary molar tooth 2 occlusal surface length
The length of the occlusal surface of an upper secondary molar tooth 2 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper primary molar tooth 2 along the anterior-posterior axis.
2021-10-06T18:43:26Z
upper primary molar tooth 2 occlusal surface length AP
upper primary molar tooth 2 occlusal surface length
The length of the occlusal surface of an upper primary molar tooth 2 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower secondary molar tooth 2 along the anterior-posterior axis.
2021-10-06T18:44:30Z
lower secondary molar tooth 2 occlusal surface length AP
lower secondary molar tooth 2 occlusal surface length
The length of the occlusal surface of a lower secondary molar tooth 2 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower primary molar tooth 2 along the anterior-posterior axis.
2021-10-06T18:45:41Z
lower primary molar tooth 2 occlusal surface length AP
lower primary molar tooth 2 occlusal surface length
The length of the occlusal surface of a lower primary molar tooth 2 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of molar tooth 3 along the medial-lateral axis.
2021-10-06T18:47:22Z
molar tooth 3 occlusal surface length ML
molar tooth 3 occlusal surface width
The length of the occlusal surface of molar tooth 3 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper molar tooth 3 along the medial-lateral axis.
2021-10-06T18:49:08Z
upper molar tooth 3 occlusal surface length ML
upper molar tooth 3 occlusal surface width
The length of the occlusal surface of an upper molar tooth 3 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower molar tooth 3 along the medial-lateral axis.
2021-10-06T18:50:18Z
lower molar tooth 3 occlusal surface length ML
lower molar tooth 3 occlusal surface width
The length of the occlusal surface of a lower molar tooth 3 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper secondary molar tooth 3 along the medial-lateral axis.
2021-10-06T18:51:20Z
upper secondary molar tooth 3 occlusal surface length ML
upper secondary molar tooth 3 occlusal surface width
The length of the occlusal surface of an upper secondary molar tooth 3 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
not a tooth
DEPRECATED upper primary molar tooth 3 occlusal surface width
true
The length of the occlusal surface of a lower secondary molar tooth 3 along the medial-lateral axis.
2021-10-06T18:55:14Z
lower secondary molar tooth 3 occlusal length ML
lower secondary molar tooth 3 occlusal surface width
The length of the occlusal surface of a lower secondary molar tooth 3 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a molar tooth 3 along the anterior-posterior axis.
2021-10-06T18:56:30Z
molar tooth 3 occlusal surface length AP
molar tooth 3 occlusal surface length
The length of the occlusal surface of a molar tooth 3 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper molar tooth 3 along the anterior-posterior axis.
2021-10-06T18:57:42Z
upper molar tooth 3 occlusal surface length AP
upper molar tooth 3 occlusal surface length
The length of the occlusal surface of an upper molar tooth 3 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower molar tooth 3 along the anterior-posterior axis.
2021-10-06T18:59:02Z
lower molar tooth 3 occlusal surface length AP
lower molar tooth 3 occlusal surface length
The length of the occlusal surface of a lower molar tooth 3 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper secondary molar tooth 3 along the anterior-posterior axis.
2021-10-06T19:00:02Z
upper secondary molar tooth 3 occlusal surface length AP
upper secondary molar tooth 3 occlusal surface length
The length of the occlusal surface of an upper secondary molar tooth 3 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower secondary molar tooth 3 along the anterior-posterior axis.
2021-10-06T19:01:18Z
lower secondary molar tooth 3 occlusal surface length AP
lower secondary molar tooth 3 occlusal surface length
The length of the occlusal surface of a lower secondary molar tooth 3 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of molar tooth 4 along the medial-lateral axis.
2021-10-06T19:03:20Z
molar tooth 4 occlusal surface length ML
molar tooth 4 occlusal surface width
The length of the occlusal surface of molar tooth 4 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper molar tooth 4 along the medial-lateral surface.
2021-10-06T19:08:31Z
upper molar tooth 4 occlusal surface length ML
upper molar tooth 4 occlusal surface width
The length of the occlusal surface of an upper molar tooth 4 along the medial-lateral surface.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower molar tooth 4 along the medial-lateral axis.
2021-10-06T19:10:10Z
lower molar tooth 4 occlusal surface length ML
lower molar tooth 4 occlusal surface width
The length of the occlusal surface of a lower molar tooth 4 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper secondary molar tooth 4 along the medial-lateral axis.
2021-10-06T19:11:15Z
upper secondary molar tooth 4 occlusal surface length ML
upper secondary molar tooth 4 occlusal surface width
The length of the occlusal surface of a lower secondry molar tooth 4 along the medial-lateral axis.
2021-10-06T19:12:12Z
lower secondary molar tooth 4 occlusal surface length ML
lower secondary molar tooth 4 occlusal surface width
The length of the occlusal surface of a lower secondry molar tooth 4 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a molar tooth 4 along the anterior-posterior axis.
2021-10-06T19:13:44Z
molar tooth 4 occlusal surface length AP
molar tooth 4 occlusal surface length
The length of the occlusal surface of a molar tooth 4 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper molar tooth 4 along the anterior-posterior axis.
2021-10-06T19:14:40Z
upper molar tooth 4 occlusal surface length AP
upper molar tooth 4 occlusal surface length
The length of the occlusal surface of an upper molar tooth 4 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower molar tooth 4 along the anterior-posterior axis.
2021-10-06T19:15:46Z
lower molar tooth 4 occlusal surface length AP
lower molar tooth 4 occlusal surface length
The length of the occlusal surface of a lower molar tooth 4 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper secondary molar tooth 4 along the anterior-posterior axis.
2021-10-06T19:16:45Z
upper secondary molar tooth 4 occlusal surface length AP
upper secondary molar tooth 4 occlusal surface length
The length of the occlusal surface of an upper secondary molar tooth 4 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower secondary molar tooth 4 along the anterior-posterior axis.
2021-10-06T19:17:44Z
lower secondary molar tooth 4 occlusal surface length AP
lower secondary molar tooth 4 occlusal surface length
The length of the occlusal surface of a lower secondary molar tooth 4 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a premolar tooth 1 along the medial-lateral axis.
2021-10-06T19:23:45Z
premolar tooth 1 occlusal surface length ML
premolar tooth 1 occlusal surface width
The length of the occlusal surface of a premolar tooth 1 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper premolar tooth 1 along the medial-lateral axis.
2021-10-06T19:25:19Z
upper premolar tooth 1 occlusal surface length ML
upper premolar tooth 1 occlusal surface width
The length of the occlusal surface of an upper premolar tooth 1 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower premolar tooth 1 along the medial-lateral axis.
2021-10-06T19:26:31Z
lower premolar tooth 1 occlusal surface length ML
lower premolar tooth 1 occlusal suface width
The length of the occlusal surface of a lower premolar tooth 1 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper secondary premolar tooth 1 along the medial-lateral axis.
2021-10-06T19:28:11Z
upper secondary premolar tooth 1 occlusal surface length ML
upper secondary premolar tooth 1 occlusal surface width
The length of the occlusal surface of an upper secondary premolar tooth 1 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface or an upper primary premolar 1 along the medial-lateral axis.
2021-10-06T19:29:34Z
upper primary premolar tooth 1 occlusal surface length ML
upper primary premolar tooth 1 occlusal surface width
The length of the occlusal surface or an upper primary premolar 1 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower secondary premolar tooth 1 along the medial-lateral axis.
2021-10-07T22:12:42Z
lower secondary premolar tooth 1 occlusal surface length ML
lower secondary premolar tooth 1 occlusal surface width
The length of the occlusal surface of a lower secondary premolar tooth 1 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower primary premolar tooth 1 along the medial-lateral axis.
2021-10-07T22:14:41Z
lower primary premolar tooth 1 occlusal surface length ML
lower primary premolar tooth 1 occlusal surface width
The length of the occlusal surface of a lower primary premolar tooth 1 along the medial-lateral axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a premolar tooth 1 along the anterior-posterior axis.
2021-10-07T22:19:59Z
premolar tooth 1 occlusal surface length AP
premolar tooth 1 occlusal surface length
The length of the occlusal surface of a premolar tooth 1 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper premolar tooth 1 along the anterior-posterior axis.
2021-10-07T22:21:59Z
upper premolar tooth 1 occlusal surface length AP
upper premolar tooth 1 occlusal surface length
The length of the occlusal surface of an upper premolar tooth 1 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower premolar tooth 1 along the anterior-posterior axis.
2021-10-07T22:23:35Z
lower premolar tooth 1 occlusal surface length AP
lower premolar tooth 1 occlusal surface length
The length of the occlusal surface of a lower premolar tooth 1 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of an upper secondary premolar tooth 1 along the anterior-posterior axis.
2021-10-07T22:27:43Z
upper secondary premolar tooth 1 occlusal surface length AP
upper secondary premolar tooth 1 occlusal surface length
The length of the occlusal surface of an upper secondary premolar tooth 1 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
The length of the occlusal surface of a lower secondary premolar tooth 1 along the anterior-posterior axis.
2021-10-07T22:31:35Z
lower secondary premolar tooth 1 occlusal tooth length AP
lower secondary premolar tooth 1 occlusal surface length
The length of the occlusal surface of a lower secondary premolar tooth 1 along the anterior-posterior axis.
https://orcid.org/0000-0003-2699-3066
<