Vision Release: 1.0.02
Jens Hansen
Yongqun Oliver He
OSCI: Ontology of Stem Cell Investigation
05-25-2018
Alexander Diehl
OSCI is a biomedical ontology in the area of stem cell investigation. OSCI imports existing ontologies such as CL, CLO, and OBI, and aims to support standardized stem cell representation, integration, and analysis.
A biomedical ontology to support stem cell investigation
OWL-DL
William Duncan
BFO OWL specification label
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
BFO OWL specification label
BFO CLIF specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
Person:Alan Ruttenberg
Really of interest to developers only
BFO CLIF specification label
BFO CLIF specification label
An annotation property that represents an ID used in the NIH LINCS project.
Oliver He, Jiangan Xie, Jie Zheng
LINCS ID
https://pubchem.ncbi.nlm.nih.gov/help.html
An annotation property that represents a PubMed BioAssay Identifier accession number.
Oliver He
PubChem AID
Oliver He
An annotation property that describes known mutation(s) about a cell.
Known mutation annotation
Cell culture condition
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
example
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
example of usage
example of usage
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
OBI_0000281
has curation status
has curation status
definition
definition
definition
textual definition
textual definition
English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
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
definition
definition
textual 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
editor note
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor
definition editor
definition editor
term editor
term editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
alternative term
alternative term
definition source
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
PERSON:Daniel Schober
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source
definition source
definition source
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
IAO:0000232
uberon
curator_notes
true
curator_notes
curator note
curator note
curator notes
curator notes
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
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
imported from
expand expression to
expand expression to
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
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
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(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)
has associated axiom(fol)
true
NHC0
code
code
code
The semantic type describes the sort of thing or category to which a concept belongs in the context of the UMLS semantic network.
P106
Conceptual Entity
Semantic Type
Semantic_Type
In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS.
Semantic_Type
Semantic_Type
Provides an alternative Preferred Name for use in some NCI systems.
P107
Conceptual Entity
Display Name
Display_Name
Display Name
Display_Name
Display_Name
The word or phrase that NCI uses by preference to refer to the concept.
P108
Conceptual Entity
Preferred Name
Preferred_Name
Preferred Name
Preferred Term
Preferred_Name
Preferred_Name
Concept Unique Identifiers, or CUIs, are concept numbers assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept.
P207
Conceptual Entity
UMLS CUI
UMLS_CUI
UMLS_CUI
UMLS_CUI
This property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake.
P322
Conceptual Entity
Contributing Source
Contributing_Source
Contributing_Source
Contributing_Source
English language definitions of what a source other than NCI means by the concept. These are limited to 1024 characters. They include information about the definition's source in a form that can easily be interpreted by software.
P325
Conceptual Entity
[source] Definition
ALT_DEFINITION
ALT_DEFINITION
ALT_DEFINITION
true
A retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding.
P366
Conceptual Entity
Legacy Concept Name
Legacy Concept Name
Legacy_Concept_Name
Design notes are notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept.
P98
Conceptual Entity
DesignNote
DesignNote
DesignNote
DesignNote
ISA alternative term
An alternative term used by the ISA tools project (http://isa-tools.org).
Requested by Alejandra Gonzalez-Beltran
https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
Person: Alejandra Gonzalez-Beltran
Person: Philippe Rocca-Serra
ISA tools project (http://isa-tools.org)
ISA alternative term
NIAID GSCID-BRC alternative term
An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC alternative term
IEDB alternative term
An alternative term used by the IEDB.
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB
IEDB alternative term
the symbol assigned by the nomenclature authority
Oliver He, Yue Liu
symbol from nomenclature authority
the full name assigned by the nomenclature authority
Oliver He, Yue Liu
full name from nomenclature authority
A GeneID in the NCBI Gene database
Oliver He, Yue Liu
NCBI GeneID
the NCBI LocusTag name of a gene
Oliver He, Yue Liu
NCBI LocusTag
the map location of a gene
Oliver He, Yue Liu
gene map location
a date of content modification
Oliver He, Yue Liu
modification date
The NCBITaxon ontology ID of an organism.
Oliver He, Yue Liu
organism NCBITaxon ID
A chromosome ID where a gene is located.
Oliver He
chromosome ID of gene
an annotation property that specifies the type of a gene
Oliver He
type of gene
an annotation property that specifies a nomenclature status
Oliver He
nomenclature status
an annotation property that shows the GO information associated with a specific gene.
Yongqun He
YH: use the convention:
GO_ID (EC: xx; Qualifier: xx; PMID: xxxxx;)
where GO_ID is a GO ID, EC is the Evidence Code, Qualifier is a specific association type, and PMID is a PubMed ID of a paper that supports the gene-GO association.
has GO association
An annotation property that represents a gene's association with PubMed publication(s).
Yongqun He
YH: use the format:
PMID: pmid1, pmid2, ...
where pmid1 and pmid2 are specfic PubMed IDs (PMIDs).
has PubMed association
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T21:59:53Z
stem cell ID
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T22:00:25Z
lot number
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T22:00:39Z
cell grade
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T22:02:49Z
contact information
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T22:08:30Z
reference publication
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T22:31:59Z
donor ID
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T22:56:10Z
donor testing method
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T22:56:31Z
donor screening method
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T22:56:59Z
source cell ID
temporal interpretation
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
temporal interpretation
temporal interpretation
https://code.google.com/p/obo-relations/wiki/ROAndTime
https://github.com/oborel/obo-relations/wiki/ROAndTime
UBPROP:0000001
uberon
external_definition
true
external_definition
This annotation property may be replaced with an annotation property from an external ontology such as IAO
external_definition
external_definition
An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
UBPROP:0000007
uberon
has_relational_adjective
true
has_relational_adjective
has_relational_adjective
has_relational_adjective
Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.
UBPROP:0000012
uberon
external_ontology_notes
true
external_ontology_notes
external_ontology_notes
external_ontology_notes
Notes on how similar or equivalent classes are represented in other ontologies.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
A metadata relation between a class and its taxonomic rank (eg species, family)
ncbi_taxonomy
has_rank
uberon
dc-contributor
true
dc-contributor
Examples of a Contributor include a person, an
organisation, or a service. Typically, the name of a
Contributor should be used to indicate the entity.
An entity responsible for making contributions to the
content of the resource.
Contributor
Contributor
contributor
Examples of a Creator include a person, an organisation,
or a service. Typically, the name of a Creator should
be used to indicate the entity.
An entity primarily responsible for making the content
of the resource.
Creator
Creator
Typically, Date will be associated with the creation or
availability of the resource. Recommended best practice
for encoding the date value is defined in a profile of
ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
A date associated with an event in the life cycle of the
resource.
Date
Date
Description may include but is not limited to: an abstract,
table of contents, reference to a graphical representation
of content or a free-text account of the content.
An account of the content of the resource.
Description
Description
Typically, Format may include the media-type or dimensions of
the resource. Format may be used to determine the software,
hardware or other equipment needed to display or operate the
resource. Examples of dimensions include size and duration.
Recommended best practice is to select a value from a
controlled vocabulary (for example, the list of Internet Media
Types [MIME] defining computer media formats).
The physical or digital manifestation of the resource.
Format
Format
The present resource may be derived from the Source resource
in whole or in part. Recommended best practice is to reference
the resource by means of a string or number conforming to a
formal identification system.
A reference to a resource from which the present resource
is derived.
Source
Source
Typically, a Subject will be expressed as keywords,
key phrases or classification codes that describe a topic
of the resource. Recommended best practice is to select
a value from a controlled vocabulary or formal
classification scheme.
The topic of the content of the resource.
Subject and Keywords
Subject and Keywords
Typically, a Title will be a name by which the resource is
formally known.
A name given to the resource.
Title
Title
Mark Miller
2018-05-11T13:47:29Z
has_alternative_id
has_alternative_id
has_broad_synonym
has_broad_synonym
database_cross_reference
database_cross_reference
Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software.
FULL_SYN
Synonym with Source Data
has exact synonym
has_exact_synonym
has_exact_synonym
has_narrow_synonym
has_narrow_synonym
has_obo_namespace
has_obo_namespace
has_related_synonym
has_related_synonym
Used to associate the concept defining a particular terminology subset with concepts that belong to this subset.
Concept_In_Subset
in subset
in_subset
in_subset
label
label
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
part_of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
has part
inheres-in_at
inheresInAt
b inheres_in c at t =Def. b is a dependent continuant & c is an independent continuant that is not a spatial region & b s-depends_on c at t. (axiom label in BFO2 Reference: [051-002])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'inheres in at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'inheres in@en(x,y,t)'.
BFO 2 Reference: Inherence is a subrelation of s-depends_on which holds between a dependent continuant and an independent continuant that is not a spatial region. Since dependent continuants cannot migrate from one independent continuant bearer to another, it follows that if b s-depends_on independent continuant c at some time, then b s-depends_on c at all times at which a exists. Inherence is in this sense redundantly time-indexed.For example, consider the particular instance of openness inhering in my mouth at t as I prepare to take a bite out of a donut, followed by a closedness at t+1 when I bite the donut and start chewing. The openness instance is then shortlived, and to say that it s-depends_on my mouth at all times at which this openness exists, means: at all times during this short life. Every time you make a fist, you make a new (instance of the universal) fist. (Every time your hand has the fist-shaped quality, there is created a new instance of the universal fist-shaped quality.)
BFO2 Reference: independent continuant that is not a spatial region
BFO2 Reference: specifically dependent continuant
(iff (inheresInAt a b t) (and (DependentContinuant a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [051-002]
inheres in at all times
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
concretized-by_st
[copied from inverse property 'concretizes at some time'] You may concretize a piece of software by installing it in your computer
[copied from inverse property 'concretizes at some time'] You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head.
[copied from inverse property 'concretizes at some time'] you may concretize a poem as a pattern of memory traces in your head
[copied from inverse property 'concretizes at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t)
[copied from inverse property 'concretizes at some time'] b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002])
concretized by at some time
concretizes_st
concretizesAt
You may concretize a piece of software by installing it in your computer
You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head.
you may concretize a poem as a pattern of memory traces in your head
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t)
b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002])
if b g-depends on c at some time t, then there is some d, such that d concretizes b at t and d s-depends_on c at t. (axiom label in BFO2 Reference: [076-001])
(forall (x y t) (if (concretizesAt x y t) (and (SpecificallyDependentContinuant x) (GenericallyDependentContinuant y) (exists (z) (and (IndependentContinuant z) (specificallyDependsOnAt x z t) (genericallyDependsOnAt y z t)))))) // axiom label in BFO2 CLIF: [075-002]
(forall (x y t) (if (genericallyDependsOnAt x y t) (exists (z) (and (concretizesAt z x t) (specificallyDependsOnAt z y t))))) // axiom label in BFO2 CLIF: [076-001]
concretizes at some time
s-depends-on_at
specificallyDependsOn
A pain s-depends_on the organism that is experiencing the pain
a gait s-depends_on the walking object. (All at some specific time.)
a shape s-depends_on the shaped object
one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
the two-sided reciprocal s-dependence of the roles of husband and wife [20
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'specifically depends on at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'specifically depends on@en(x,y,t)'.
BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
BFO2 Reference: specifically dependent continuant\; process; process boundary
To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001])
If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001])
If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002])
an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002])
if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002])
(forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002]
(forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002]
(forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001]
(forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002]
(forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001]
specifically depends on at all times
located-at-r_st
occupiesSpatialRegionAt
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
BFO2 Reference: independent continuant
BFO2 Reference: spatial region
b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])
every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002])
if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001])
(forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002]
(forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002]
(forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001]
occupies spatial region at some time
http://www.ebi.ac.uk/efo/has_quality
has_quality
exists-at
existsAt
BFO2 Reference: entity
BFO2 Reference: temporal region
b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
exists at
o-has-part
hasOccurrentPart
[copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life
[copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
[copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
[copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
[copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
(iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]
has occurrent part
o-has-ppart
hasProperOccurrentPart
[copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
has proper occurrent part
r-location-of_st
[copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant
[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region
[copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])
has spatial occupant at some time
has-s-dep_st
[copied from inverse property 'specifically depends on at some time'] A pain s-depends_on the organism that is experiencing the pain
[copied from inverse property 'specifically depends on at some time'] a gait s-depends_on the walking object. (All at some specific time.)
[copied from inverse property 'specifically depends on at some time'] a shape s-depends_on the shaped object
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
[copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
[copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
[copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
[copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
[copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
[copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
[copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
[copied from inverse property 'specifically depends on at some time'] the two-sided reciprocal s-dependence of the roles of husband and wife [20
[copied from inverse property 'specifically depends on at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)
[copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
[copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
[copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
[copied from inverse property 'specifically depends on at some time'] BFO2 Reference: specifically dependent continuant\; process; process boundary
[copied from inverse property 'specifically depends on at some time'] To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
has specific dependent at some time
occupied-by
[copied from inverse property 'occupies spatiotemporal region'] BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
[copied from inverse property 'occupies spatiotemporal region'] p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])
has spatiotemporal occupant
occupies
occupiesSpatiotemporalRegion
BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])
occupies spatiotemporal region
o-part-of
occurrentPartOf
Mary’s 5th birthday occurrent_part_of Mary’s life
The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
the first set of the tennis match occurrent_part_of the tennis match.
[copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
BFO2 Reference: occurrent
b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001])
occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002])
occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001])
occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001])
occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001])
(forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001]
(forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001]
(forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001]
(forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001]
(forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002]
part of occurrent
o-ppart-of
properOccurrentPartOf
[copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
(iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001]
proper part of occurrent
t-part-of
temporalPartOf
the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
the process boundary which separates the 3rd and 4th years of your life.
your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002])
(forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002]
(iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001]
(iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003]
temporal part of
st-projects-onto-s_st
projects onto spatial region at some time
s-projection-of-st_st
spatial projection of spatiotemporal at some time
st-projects-onto-t
projects onto temporal region
t-projection-of-st
temporal projection of spatiotemporal
spans
occupiesTemporalRegion
p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
occupies temporal region
span-of
spanOf
[copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
has temporal occupant
during-which-exists
[copied from inverse property 'exists at'] BFO2 Reference: entity
[copied from inverse property 'exists at'] BFO2 Reference: temporal region
[copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
during which exists
bearer-of_at
bearerOfAt
b bearer_of c at t =Def. c s-depends_on b at t & b is an independent continuant that is not a spatial region. (axiom label in BFO2 Reference: [053-004])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'bearer of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'bearer of@en(x,y,t)'.
BFO2 Reference: independent continuant that is not a spatial region
BFO2 Reference: specifically dependent continuant
(iff (bearerOfAt a b t) (and (specificallyDependsOnAt b a t) (IndependentContinuant a) (not (SpatialRegion a)) (existsAt b t))) // axiom label in BFO2 CLIF: [053-004]
bearer of at all times
has-d_at
hasDispositionAt
a has_disposition b at t =Def. b disposition_of a at t. (axiom label in BFO2 Reference: [069-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has disposition at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has disposition@en(x,y,t)'.
(iff (hasDispositionAt a b t) (dispositionOf b a t)) // axiom label in BFO2 CLIF: [069-001]
has disposition at all times
has-s-dep_at
has specific dependent at all times
s-depends-on_st
specificallyDependsOn
A pain s-depends_on the organism that is experiencing the pain
a gait s-depends_on the walking object. (All at some specific time.)
a shape s-depends_on the shaped object
one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
the two-sided reciprocal s-dependence of the roles of husband and wife [20
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)
BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
BFO2 Reference: specifically dependent continuant\; process; process boundary
To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001])
If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001])
If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002])
an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002])
if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002])
(forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002]
(forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002]
(forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001]
(forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002]
(forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001]
specifically depends on at some time
c-part-of_st
continuantPartOfAt
Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
[copied from inverse property 'has continuant part at some time'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t)
BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
BFO2 Reference: continuant
BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
[copied from inverse property 'has continuant part at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t)
b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001])
continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002])
continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001])
continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001])
continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001])
if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002])
(forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002]
(forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002]
(forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001]
(forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001]
(forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001]
(forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001]
(iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001]
part of continuant at some time
c-has-part_st
hasContinuantPartAt
[copied from inverse property 'part of continuant at some time'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
[copied from inverse property 'part of continuant at some time'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t)
[copied from inverse property 'part of continuant at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t)
[copied from inverse property 'part of continuant at some time'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
[copied from inverse property 'part of continuant at some time'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuant
[copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
[copied from inverse property 'part of continuant at some time'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
(iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001]
has continuant part at some time
c-part-of-object_at
[copied from inverse property 'has continuant part at all times'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)
This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'
[copied from inverse property 'has continuant part at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'.
part of continuant at all times that whole exists
c-has-part-object_at
[copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
[copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)
This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'
[copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.
[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant
[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
[copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
has continuant part at all times that part exists
a 'derives from' object property between an entity (in CLO case, cell line) and a disease in a patient where the entity is derived from some cell in the patient who has the disease.
This is a short cut relation that represents:
'derived from' some (cell and ('part of' some 'organism' and ('has disease' some disease)))
Yongqun He
In most cases, the patient in the relation is used to refer human patient. However, an animal patient (or veterinary patient) can also be referred.
derives from patient having disease
an object property that specifies a cell line repository for a specifc cell line.
SS, YH, UV, SS
is in cell line repository
an object property that represents a relation between a cell line cell and a disease.
Asiyah Yu Lin, Yongqun He
This object property is largely equivalent to the previous term 'is model for' (http://www.ebi.ac.uk/cellline#is_model_for).
is disease model for
a 'cell line cell derives from' object property between an entity (e.g., cell line cell in CLO) and an organism where the cell line cell is derived from some cell from the organism.
In CLO, this is a short cut relation that represents:
'derived from' some (cell and ('part of' some organism))
derived from organism
derived from cell
has measurement unit label
is about
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
We will try to build it back up by elaborating the various subproperties that are more precisely defined.
Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.
g denotes r =def
r is a portion of reality
there is some c that is a concretization of g
every c that is a concretization of g specifically denotes r
person:Alan Ruttenberg
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
m is a quality measurement of q at t when
q is a quality
there is a measurement process p that has specified output m, a measurement datum, that is about q
8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important]
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
--
From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009]
unit of measure is a quality, e.g. the length of a ruler.
[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label]
[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory]
a represents b means either a denotes b or a describes
describe:
a describes b means a is about b and a allows an inference of at least one quality of b
We have had a long discussion about denotes versus describes.
From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully.
a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
From the second meeting on IAO:
An attempt at defining assay using Barry's "reliability" wording
assay:
process and has_input some material entity
and has_output some information content entity
and which is such that instances of this process type reliably generate
outputs that describes the input.
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
Alan Ruttenberg
is quality measurement of
relates a process to a time-measurement-datum that represents the duration of the process
Person:Alan Ruttenberg
is duration of
inverse of the relation of is quality measurement of
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
Person:Alan Ruttenberg
is quality measured as
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
Alan Ruttenberg
has time stamp
relates a time stamped measurement datum to the measurement datum that was measured
Alan Ruttenberg
has measurement datum
is_supported_by_data
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
OBI
OBI
Philly 2011 workshop
is_supported_by_data
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
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
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
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
has grain
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
PERSON: Alan Ruttenberg
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
has grain
objective_achieved_by
This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
OBI
OBI
objective_achieved_by
has category label
A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale.
has category label
specifies value of
A relation between a value specification and an entity which the specification is about.
specifies value of
has value specification
A relation between an information content entity and a value specification that specifies its value.
PERSON: James A. Overton
OBI
has value specification
a 'part of continuant at some time' relation that incides a genome belongs to a organism.
Yongqun He, Bin Zhao
is genome of organism
a relation between a gene and the organism where this gene belongs to the organism in nature. It does not include a foreign gene that is transferred to an organism by a genetic engineering method.
Oliver He, Yue Liu
is gene of organism
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T22:02:00Z
produced by
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T22:07:22Z
provided by
inheres in
this fragility inheres in this vase
this red color inheres in this apple
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
'inheres in at all times'
inheres_in
inheres in
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
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
bearer_of
is bearer of
bearer of
bearer_of
is bearer of
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
has_participant
is concretized as
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
concretized by at some time
http://purl.obolibrary.org/obo/obi.owl
is concretized as
concretizes
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
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.
http://purl.obolibrary.org/obo/obi.owl
It is recommended to not use this if possible in OMRSE. According to OntoBee this relation has been obsoleted and replaced with 'concretization of at all times'. As of Dec. 2, 2013 iao-main still uses this relation.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
function of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
has role
derives from
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
derives from
derives_from
derives into
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
located in
Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
has plasma membrane part
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
A is spatially_disjoint_from B if and only if they have no parts in common
spatially disjoint from
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
develops from
develops into
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.
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
capable of part of
x adjacent to y if and only if x and y share a boundary
adjacent to
move to BFO?
Allen
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporal relation
inverse of starts with
Chris Mungall
Allen
starts
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
developmentally preceded by
Inverse of developmentally preceded by
developmentally succeeded by
A mereological relationship or a topological relationship
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
developmentally related to
functionally related to
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 the potential to develop into y iff x develops into y or if x is capable of developing into y
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
has potential to directly develop into
This relation groups causal relations between material entities and causal relations between processes
causally related to
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in
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
Inverse of 'causal agent in'
has causal agent
A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
related via dependence to
A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).
has_low_plasma_membrane_amount
http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)
lacks_plasma_membrane_part
has_disease_location
has measurement value
has specified numeric value
A relation between a value specification and a number that quantifies it.
A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
PERSON: James A. Overton
OBI
has specified numeric value
has specified value
A relation between a value specification and a literal.
This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
OBI
has specified value
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T22:01:30Z
date placed in storage
entity
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
true
continuant
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
true
occurrent
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
true
ic
IndependentContinuant
independent continuant
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
true
true
true
s-region
SpatialRegion
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
true
true
true
t-region
TemporalRegion
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
true
true
true
st-region
SpatiotemporalRegion
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal region
true
process
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
true
disposition
Disposition
disposition
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocitosis and exocitosis
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
true
realizable
RealizableEntity
realizable entity
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
true
quality
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
true
sdc
SpecificallyDependentContinuant
specifically dependent continuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of 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
true
role
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
true
3d-s-region
ThreeDimensionalSpatialRegion
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
true
gdc
GenericallyDependentContinuant
generically dependent continuant
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
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
true
function
Function
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
true
p-boundary
ProcessBoundary
the boundary between the 2nd and 3rd year of your life.
p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
true
material
MaterialEntity
material entity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
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
true
immaterial
ImmaterialEntity
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
true
0d-t-region
ZeroDimensionalTemporalRegion
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
true
anatomical structure
true
material anatomical entity
true
cell part
true
deoxyribonucleic acid
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
deoxyribonucleic acid
true
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
molecular entity
true
atom
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
atom
true
nucleic acid
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
nucleic acid
true
macromolecule
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
polymer
macromolecule
true
cell line cell
A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters
A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures.
cell line cell
true
a role that inheres in a cell line repository organization.
SS, YH
cell line repository role
true
an organization that serves as a repository of cell lines.
SS, YH
cell line repository
true
cell line
He, Tong-Chuan, et al., Identification of c-MYC as a target of the APC pathway. Science 281.5382 (1998): 1509-1512.: "To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene".
Note that common usage in the literature is often of the form "a human colorectal cancer cell line", as seen above. But such references to studies in "a line" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'.
A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
In the spring of 2013, a working group comprised of domain experts and representatives from CLO, OBI, CL, and ReO worked to establish a consensus model and definitions of cultured cells across these efforts. This included a careful characterization of how the term 'cell line' should be defined and applied. Notes about this work and its outcomes can be found on the CLO wiki here:
http://code.google.com/p/clo-ontology/wiki/Cell_Lines
MB, SS, JZ, MAH, BP, CS, YH
The term 'line' is used when a culture has undergone an intentional experimental process to establish a more uniform and stable population of cells (see 'establishing cell line'). This will require one or more passages, but may involve additional selection processes. Through such passaging and/or selection processes, the resulting 'line' attains some level of genetic stability and compositional homogeneity which is typically absent in primary cultures. Because of their relative homogeneity, ‘lines’ are capable of being characterized and stably propagated over a period of time. A new *type* of cell line can be established not only through the passaging/selection of a primary culture, but also through experimental modifications of existing lines (e.g. immortalization, stable genetic modifications, drug selection for a resistant subset, etc.).
The definition provided here establishes the 'scale' of cell populations that qualify as cell lines - specifically those with a shared propagation history in culture. In this way, the 'cell line' class demarcates populations that represent what researchers actually use in the practice of science - e.g. as inputs to culturing, experimentation, and sharing. The definition is such that cell lines will exhibit important attributes. For example, they will have a relatively homogenous cell type composition as they have experienced similar selective pressures due to their continuous co-propagation. In addition, these populations can also be characterized by a passage number, again owing to their common passaging history. As defined here, 'cell line' can refer to a population of cells in active culture, applied experimentally, or stored in a quiescent state for future use.
cell line
true
LPC-1021
only one copy of the SMN2 gene; homozygous for deletion of exons 7 and 8 of the SMN1 gene
Chao Pang, Oliver He, Daniel Cooper
GM00232
http://lincsportal.ccs.miami.edu/cells/#/view/LPC-1021
http://web.expasy.org/cellosaurus/CVCL_Y965
GM-232
SPINAL MUSCULAR ATROPHY I; SMA1
Cell center: NeuroLINCS
Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository
GM00232 cell
OMIM: 253300
RRID:CVCL_Y965
true
A cell line cell that is cultured in vitro and possesses two capabilities: (1) it can self-renew, which means that it can divide indefinitely while remaining in an undifferentiated state; and (2) it is pluripotent or multipotent, which means that it can differentiate to form a specialized cell type.
Yongqun He, Sirarat Sarntivijai, Alexander Diehl
WEB: https://en.wikipedia.org/wiki/Stem-cell_line
While stem cells hold great promise for biomedical research, the in vitro propagation and maintenance of these cells in an undifferentiated state is essential. Reference:
https://www.atcc.org/~/media/7E031EF950594BC3B85A411AE1DC9684.ashx
stem cell line cell
true
A stem cell line cell that is derived from mouse.
YH
mouse stem cell line cell
true
A mouse stem cell line cell that is derived from a mouse neural progenitor cell and capable of differentiation in vitro.
YH
immortalized mouse neural progenitor cell
mouse neural progenitor cell line cell
true
1353
http://web.expasy.org/cellosaurus/CVCL_4511
http://www.sigmaaldrich.com/catalog/product/sigma/07062902
An immortalised mouse neural progenitor cell line cell that is capable of differentiation in vitro and is established by retorviral-mediated transduction of the avian myc oncogene into mitotic progenitor cells of neonatal mouse cerrebellum. Mouse strain CD1 x C57BL/6.
BAO, YH
C17.2 cell
BAO: BAO_0030046
true
YH, AD
https://en.wikipedia.org/wiki/Embryonic_stem_cell
A stem cell line cell that is dervied from an embryotic stem cell, a pluripotent stem cell derived from the inner cell mass of a blastocyst, an early-stage perimplantation embryo.
ES cell line cell
embryonic stem cell line cell
true
YH, AD
hES cell line cell
https://en.wikipedia.org/wiki/Embryonic_stem_cell
An embryonic stem cell line cell that is dervied from a cell in human embryo.
hESC line cell
human embryonic stem cell line cell
true
YH, AD
https://discovery.lifemapsc.com/stem-cell-differentiation/in-vitro-cells/inner-cell-mass-homo-sapiens-line-h1-wa01-wicell-research-institute-inc
H1-hESC
A human ES cell line cell that expresses cell surface markers specific to undifferentiated nonhuman primate ES and human EC cells: : stage-specific embryonic antigen (SSEA)–3, SSEA-4, TRA-l-60, TRA-1- 81, and alkaline phosphatase. It has a normal 46, XY karyotype, O+ blood type. Teratomas are formed upon cell injection into SCID mice. These teratomas include cells from all three germ layers.
Line H1 cell
true
Oliver He
A primary cultured cell that is derived from fibroblast cell in vivo
primary cultured fibroblast cell
true
Oliver He
A primary cultured fibroblast cell that is from human
primary cultured human fibroblast cell
true
YH, AD
https://en.wikipedia.org/wiki/Stem-cell_line
A stem cell line cell that is multipotent and is isolated and prepared from an juvenile or adult tissue.
adult stem cell line cell
true
YH, AD
https://en.wikipedia.org/wiki/Stem-cell_line
An adult stem cell line cell that is isolated and prepared using bone marrow tissue and is able to generate all cells of the immune system and all blood cell types.
Of the types of adult stem cells have successfully been isolated and identified, only mesenchymal stem cells can successfully be grown in culture for long periods of time. Hematopoietic stem cells are difficult to grow and propagate in vitro.[4] Identifying methods for maintaining hematopoietic stem cells in vitro is an active area of research. Reference: https://en.wikipedia.org/wiki/Stem-cell_line
hematopoetic stem cell line cell
true
YH
https://en.wikipedia.org/wiki/Stem-cell_line
An adult stem cell line cell that is isolated and prepared using umbilical cord blood, amniotic fluid, and adipose tissue and can generate a number of cell types, including osteoblasts, chondrocytes, and adipocytes.
MSC line cell
mesenchymal stem cell line cell
true
YH, AD
https://en.wikipedia.org/wiki/Stem-cell_line
A mesenchymal stem cell line cell that is isolated and prepared using umbilical cord blood.
umbilical cord mesenchymal stem cell line cell
true
YH, AD
https://en.wikipedia.org/wiki/Embryonic_stem_cell
https://en.wikipedia.org/wiki/Induced_pluripotent_stem_cell
https://www.ncbi.nlm.nih.gov/pubmed/16904174
A stem cell line cell that is pluripotent and is generated from an adult somatic cell.
iPS cell
iPSC
induced pluripotent stem cell line cell
true
YH, AD
An induced pluripotent stem cell line cell that is derived from a human cell.
human iPS cell line cell
human induced pluripotent stem cell line cell
true
LES-1001
LINCS team, YH
http://lincsportal.ccs.miami.edu/cells/#/view/LES-1001
https://discovery.lifemapsc.com/stem-cell-differentiation/in-vitro-cells/inner-cell-mass-homo-sapiens-line-h9-wa09-wicell-research-institute-inc
This human ES cell line expresses cell surface markers specific to undifferentiated nonhuman primate ES and human EC cells: stage-specific embryonic antigen (SSEA)–3, SSEA-4, TRA-l-60, TRA-1- 81, and alkaline phosphatase. It has a normal 46, XX karyotype. Teratomas are formed upon cell injection into SCID mice. These teratomas include cells from all three germ layers.
H9 ES cell
true
LES-1002
LINCS team, YH
http://lincsportal.ccs.miami.edu/cells/#/view/LES-1002
https://grants.nih.gov/stem_cells/registry/current.htm?id=34
HUES 3
HUES3 ES cell
true
YH
mES cell line cell
https://en.wikipedia.org/wiki/Embryonic_stem_cell
A embryotic stem cell line cell that is dervied from a cell in mouse embryo.
mESC line cell
mouse embryonic stem cell line cell
true
YH, AD
https://en.wikipedia.org/wiki/Somatic_cell_nuclear_transfer#Stem_cell_research
A stem cell line cell that is dervied from using the somatic cell nuclear transfer method.
SCNT-derived stem cell line cell
somatic cell nuclear transfer-derived stem cell line cell
true
YH
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3772789/
a human embryonic stem cell line cell that is derived by somatic cell nuclear transfer
human embryonic stem cell line cell derived by SCNT
human embryonic stem cell line cell derived by somatic cell nuclear transfer
true
true
human fibroblast-iPS cell line cell
human fibroblast-induced pluripotent stem cell line cell
true
Oliver He
A primary cultured cell that is derived from in vivo connective tissue cell
primary cultured connective tissue cell
true
LPC-1014
Donor subject has two copies of the SMN2 and is heterozygous for deletion of exons 7 and 8 in the SMN1 gene
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository
GM03814 cell
true
LPC-1015
Unclassified
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository
GM02183 cell
true
LPC-1016
CAG length Allele 1 = 18; Allele 2 = 17
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository
ND30625 cell
true
LPC-1017
C9orf72; repeat number not indicated
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Wasington University; Cell provider catalog number: Wasington University
F09128 cell
true
LPC-1018
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
F09229 cell
true
LPC-1019
C9orf72; repeat number not indicated
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Wasington University; Cell provider catalog number: Wasington University
F10-330 cell
true
LPC-1020
C9orf72; repeat number not indicated
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Wasington University; Cell provider catalog number: Wasington University
F09152 cell
true
LPC-1022
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository
83 Fibroblast cell
true
LPC-1023
donor subject has 2 copies of the SMN2 gene and is homozygous for deletion of exons 7 and 8 of the SMN1 gene
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository
GM09677 cell
true
LPC-1024
Daniel Cooper, Oliver He
Cell center: DToxS
Cell provider: ISMMS; Cell provider catalog number: ISMMS
MSF01 cell
true
LPC-1025
Daniel Cooper, Oliver He
Cell center: DToxS
Cell provider: ISMMS; Cell provider catalog number: ISMMS
MSF02 cell
true
LPC-1026
Daniel Cooper, Oliver He
Cell center: DToxS
Cell provider: ISMMS; Cell provider catalog number: ISMMS
MSF03 cell
true
LPC-1028
Daniel Cooper, Oliver He
Cell center: DToxS
Cell provider: ISMMS; Cell provider catalog number: ISMMS
MSF05 cell
true
LPC-1029
Daniel Cooper, Oliver He
Cell center: DToxS
Cell provider: ISMMS; Cell provider catalog number: ISMMS
MSF06 cell
true
LPC-1031
Daniel Cooper, Oliver He
Cell center: DToxS
Cell provider: ISMMS; Cell provider catalog number: ISMMS
MSF08 cell
true
LPC-1032
Daniel Cooper, Oliver He
Cell center: DToxS
Cell provider: ISMMS; Cell provider catalog number: ISMMS
MSF09 cell
true
LPC-1033
Daniel Cooper, Oliver He
Cell center: DToxS
Cell provider: ISMMS; Cell provider catalog number: ISMMS
MSF10 cell
true
LPC-1044
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository
GM05400 cell
true
LPC-1054
ALS-Sporadic
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
W14-C146 cell
true
LPC-1055
ALS-SOD1
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
F13-C004 cell
true
LPC-1056
ALS-Sporadic
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
W15-C166 cell
true
LPC-1057
ALS-SOD1
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
SAB-701-022 cell
true
LPC-1058
ALS-Sporadic
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
W14-C138 cell
true
LPC-1059
ALS-Sporadic
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
W14-C152 cell
true
LSC-1002
Donor subject has two copies of the SMN2 and is heterozygous for deletion of exons 7 and 8 in the SMN1 gene
mTeSR1, Growth Factor Reduced Matrigel
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS14iCTR-n6
CS14iCTR-n6 cell
true
LSC-1003
Unclassified
mTeSR1, Growth Factor Reduced Matrigel
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS83iCTR-33n1
CS83iCTR-33n1 cell
true
LSC-1004
CAG length Allele 1 = 18; Allele 2 = 17
mTeSR1, Growth Factor Reduced Matrigel
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS25iCTR-18n2
CS25iCTR-18n2 cell
true
LSC-1005
C9orf72; repeat number not indicated
mTeSR1, Growth Factor Reduced Matrigel
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS28iALS-n2A
CS28iALS-n2A cell
true
LSC-1006
C9orf72; repeat number not indicated
mTeSR1, Growth Factor Reduced Matrigel
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS29iALS-n1N
CS29iALS-n1N cell
true
LSC-1007
C9orf72; repeat number not indicated
mTeSR1, Growth Factor Reduced Matrigel
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS30iALS-n1N
CS30iALS-n1N cell
true
LSC-1008
C9orf72; repeat number not indicated
mTeSR1, Growth Factor Reduced Matrigel
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS52iALS-n6A
CS52iALS-n6A cell
true
LSC-1009
only one copy of the SMN2 gene; homozygous for deletion of exons 7 and 8 of the SMN1 gene
mTeSR1, Growth Factor Reduced Matrigel
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS32iSMA-n3
CS32iSMA-n3 cell
true
LSC-1011
Unknown
mTeSR1, Growth Factor Reduced Matrigel
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS83iSMA-n5
CS83iSMA-n5 cell
true
LSC-1012
donor subject has 2 copies of the SMN2 gene and is homozygous for deletion of exons 7 and 8 of the SMN1 gene
mTeSR1, Growth Factor Reduced Matrigel
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS77iSMA-n5
CS77iSMA-n5 cell
true
LSC-1013
none/healthy
human pluripotent stem cell medium, includign mTeSR
Daniel Cooper, Oliver He
Cell center: DToxS
MSN01-3 cell
true
LSC-1014
none/healthy
human pluripotent stem cell medium, includign mTeSR
Daniel Cooper, Oliver He
Cell center: DToxS
MSN03-7 cell
true
LSC-1015
none/healthy
human pluripotent stem cell medium, includign mTeSR
Daniel Cooper, Oliver He
Cell center: DToxS
MSN05-1 cell
true
LSC-1016
none/healthy
human pluripotent stem cell medium, includign mTeSR
Daniel Cooper, Oliver He
Cell center: DToxS
MSN06-7 cell
true
LSC-1017
none/healthy
human pluripotent stem cell medium, includign mTeSR
Daniel Cooper, Oliver He
Cell center: DToxS
MSN02-4 cell
true
LSC-1018
none/healthy
human pluripotent stem cell medium, includign mTeSR
Daniel Cooper, Oliver He
Cell center: DToxS
MSN08-13 cell
true
LSC-1019
none/healthy
human pluripotent stem cell medium, includign mTeSR
Daniel Cooper, Oliver He
Cell center: DToxS
MSN09-4 cell
true
LSC-1020
none/healthy
human pluripotent stem cell medium, includign mTeSR
Daniel Cooper, Oliver He
Cell center: DToxS
MSN10-1 cell
true
LSC-1021
Daniel Cooper, Oliver He
Cell center: BROAD_T
FIBRNPC cell
true
LSC-1022
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
CS14isALS-Tn16 cell
true
LSC-1023
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
CS04iALS-SOD1H44Rn3 cell
true
LSC-1024
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
CS00iCTR-n2 cell
true
LSC-1025
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
CS29iALS-C9n1 cell
true
LSC-1026
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
CS30iALS-C9n1 cell
true
LSC-1027
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
CS166isALS-Tn2 cell
true
LSC-1028
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
CS22iALS-SOD1I113Tn2 cell
true
LSC-1029
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
CS138isALS-Tn1 cell
true
LSC-1030
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
CS152isALS-Tn2 cell
true
LSC-1031
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
CS28iALS-C9n2 cell
true
LSC-1032
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
CS52iALS-C9n6 cell
true
LSC-1033
Daniel Cooper, Oliver He
Cell center: NeuroLINCS
CS11iALS-SOD1I113Tn10 cell
true
cell
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
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
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
cell type
EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000324
true
true
primary cultured cell
A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged.
primary cultured cell
true
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
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
true
true
neuronal receptor cell (sensu Animalia)
cell
neuronal receptor cell
true
true
cell
migratory cranial neural crest cell
true
cultured cell
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
cell
Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture.
cultured cell
true
cell
migratory trunk neural crest cell
true
germline stem cell
cell
germ line stem cell
true
true
FMA:72290
MA:0002765
VHOG:0001531
ncithesaurus:Spermatogenic_Cell
cell
male germ cell
true
cell
male germ line stem cell
true
true
Female germ cell is a germ cell that supports female gamete production.
MA:0000388
VHOG:0001530
ncithesaurus:Egg
cell
female germ cell
true
cell
female germ line stem cell
true
true
A cell that will develop into a neuron often after a migration phase.
BTO:0000930
FBbt:00005146
FMA:70563
cell
neuroblast
true
true
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
stem cell
true
A stem cell that self-renews as well as give rise to a single mature cell type.
FMA:70569
unipotent stem cell
unipotential stem cell
cell
single fate stem cell
true
cell
epithelial fate stem cell
true
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
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
true
true
A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring.
cell
Originally this term had some plant germ line cell children.
germ line cell
true
Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors.
BTO:0002881
CALOHA:TS-2360
FMA:86684
NSC
neural stem cell
cell
neuronal stem cell
true
true
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
multi fate stem cell
true
true
A stem cell from which all cells of the body can form.
FMA:84790
totipotential stem cell
cell
totipotent stem cell
true
A precursor cell with a limited number of potential fates.
BTO:0000125
FMA:84782
blast cell
cell
define using PATO mulit-potent or oligopotent?
non-terminally differentiated cell
true
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
myoblast
true
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.
James Malone
Tomasz Adamusiak
mouse embryonic fibroblast
primary dermal fibroblast
BTO:0000452
CL:0000057
NIFSTD:nlx_cell_20090201
BTO:0000452
CALOHA:TS-0362
FMA:63877
VHOG:0001482
cell
A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules.
A connective-tissue cell of mesenchymal origin that secretes proteins and especially molecular collagen from which the extracellular fibrillar matrix of connective tissue forms.
A large, flat, oval cell found in connective tissue and responsible for the formation of fibers.
These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative.
fibroblast
EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000496
URI: http://www.ebi.ac.uk/cellline#fibroblast
true
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
epithelial cell
true
cell
duct epithelial cell
true
true
cell
branched duct epithelial cell
true
cell
columnar/cuboidal epithelial cell
true
true
CALOHA:TS-1249
cell
squamous epithelial cell
true
cell
stratified epithelial cell
true
true
A cell which moves among different tissues of the body, via blood, lymph, or other medium.
cell
circulating cell
true
BTO:0004299
lung epithelial cell
cell
epithelial cell of lung
true
cell
germ line stem cell (sensu Vertebrata)
true
FBbt:00004861
cell
germ line stem cell (sensu Nematoda and Protostomia)
true
FBbt:00004929
cell
male germ line stem cell (sensu Nematoda and Protostomia)
true
true
FBbt:00004873
cell
female germ line stem cell (sensu Nematoda and Protostomia)
true
true
spermatogonial stem cell
cell
male germ line stem cell (sensu Vertebrata)
true
true
cell
female germ line stem cell (sensu Vertebrata)
true
true
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
The term "neuroepithelial cell" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710).
sensory epithelial cell
true
true
true
Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
BTO:0001037
FBbt:00005124
FMA:84649
WBbt:0005759
cell
sensory neuron
true
FMA:72552
cell of surface ectoderm
surface ectoderm cell
cell
surface ectodermal cell
true
Ectoderm destined to be nervous tissue.
neurectoderm cell
cell
neurectodermal cell
true
A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. 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
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
true
true
true
A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules.
CALOHA:TS-2085
FMA:86494
cell
glandular epithelial cell
true
true
true
A cell that specializes in controlled release of one or more substances.
BTO:0003659
FMA:86916
cell
secretory cell
true
A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct.
FMA:16014
cell
exocrine cell
true
A cell whose primary function is to shorten.
cell
contractile cell
true
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
muscle cell
true
true
true
true
A somatic cell located in skeletal muscle.
BTO:0004392
CALOHA:TS-2158
FMA:9727
skeletal muscle cell
cell
cell of skeletal muscle
true
cell
receptor cell
true
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
chemoreceptor cell
true
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
taste receptor cell
true
true
true
true
true
true
A cell whose function is determined by the generation or the reception of an electric signal.
cell
electrically active cell
true
A cell that moves by its own activities.
cell
motile cell
true
A cell of the outer of the three germ layers of the embryo.
FMA:72549
ectoderm cell
cell
ectodermal cell
true
A cell of the middle germ layer of the embryo.
FMA:72554
mesoblast
mesoderm cell
cell
mesodermal cell
true
A cell of the inner of the three germ layers of the embryo.
FMA:72555
endoderm cell
cell
endodermal cell
true
cell
keratinizing barrier epithelial cell
true
true
true
cell
stratified squamous epithelial cell
true
true
cell
eukaryotic cell
true
An epithelial cell found in the trachea.
CL:1000474
FMA:74793
tracheocyte
cell
This class is for the vertebrate tracheal structure. For the analagous insect cell type, see 'respiratory tube epithelial cell'
tracheal epithelial cell
true
cell
keratin accumulating cell
true
An epidermal cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell.
CL:0002185
BTO:0000667
CALOHA:TS-0500
FMA:62879
keratinized cell of epidermis
malpighian cell
cell
Keratinocytes are reportedly CDw210a-negative, CDw210b-positive, CD281-positive, CD282-positive, CD285-positive, IL22Ra1-positive, Human keratinocytes are reportedly capable of secreting BD-2, BD-3, hCAP-18, CXCL1, CXCL5, CXCL8, elafin, MMP-3, NGAL, PDGF-A, S100A7, S100A8, and S100A9. Transcription factors: STAT3-positive.
keratinocyte
true
true
cell
metanephric mesenchyme stem cell
true
A cell that is specialised to accumulate a particular substance(s).
cell
stuff accumulating cell
true
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
migratory neural crest cell
true
true
An embryonic cell that develops into a nerve cell or neuron.
cell
neuroblast (sensu Vertebrata)
true
neuroblast
cell
neuroblast (sensu Nematoda and Protostomia)
true
A specialized mesenchymal cell that resides in the dermal papilla located at the bottom of hair follicles. This cell plays a pivotal roles in hair formation, growth, and cycling.
cell
Are these really all stem cells?
hair follicle dermal papilla cell
true
cell
extraembryonic cell
true
true
A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.
cell
epiblast cell
true
ncithesaurus:Blastemal_Cell
blastema cell
cell
blastemal cell
true
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
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
true
true
cell
hair matrix stem cell
true
cell
stratified epithelial stem cell
true
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
epidermal cell
true
cell
tracheoblast
true
cell
nephrogenic mesenchyme stem cell
true
A cell whose function is determined by its response to an electric signal.
cell
electrically responsive cell
true
A cell that initiates an electrical signal and passes that signal to another cell.
cell
electrically signaling cell
true
FBbt:00005148
cell
neuroepidermoblast
true
An epithelial fate stem cell found in flatworms.
BTO:0003039
cell
seam cell
true
FBbt:00004903
cell
follicle stem cell
true
FBbt:00005147
cell
neuroglioblast
true
true
FBbt:00005149
cell
ganglion mother cell
true
A neuron which conveys sensory information centrally from the periphery.
FMA:87653
input neuron
cell
afferent neuron
true
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
These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.
neuron
neuron
true
true
true
cell
animal cell
true
A mesenchymal stem cell capable of developing into blood vessel endothelium.
angioblast
chondroplast
cell
These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive.
angioblastic mesenchymal cell
true
experimentally modified cell in vitro
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
cell
This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12
experimentally modified cell in vitro
true
true
The reproductive cell in multicellular organisms.
BTO:0000535
VHOG:0001534
WBbt:0006796
cell
germ cell
true
An elongated, spindle-shaped, cell that is located between the basal lamina and the plasmalemma of a muscle fiber. These cells are mostly quiescent, but upon activation they divide to produce cells that generate new muscle fibers.
cell
Skeletal muscle satellite cells are not traditionally referred to as myoblasts. They are a heterogeneous population whose division, following activiation, contributes to the formation of skeletal muscle fibers and to maintenance of the skeletal muscle statelite cell population.
skeletal muscle satellite cell
true
true
Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament.
BTO:0000939
FMA:62516
cell
basal cell
true
cell
neuroglioblast (sensu Nematoda)
true
A non-terminally differentiated cell that is capable of developing into a muscle cell.
cell
muscle precursor cell
true
true
Epithelial cells derived from neural plate and neural crest.
neuroepithelial cell
BTO:0004301
FMA:70557
cell
The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098).
neurecto-epithelial cell
true
true
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
somatic stem cell
true
true
A cell of a hematopoietic lineage.
BTO:0000574
CALOHA:TS-2017
FMA:70366
FMA:83598
haematopoietic cell
haemopoietic cell
hemopoietic cell
cell
hematopoietic cell
true
true
A hematopoietic stem cell that has plasma membrane part Kit-positive, SCA-1-positive, CD150-positive and CD34-negative.
LSK stem cell
Sca1-positive hematopoietic stem cell
cell
Cell markers are associated with mouse hematopoietic stem cell. Originally described in the dendritic cell ontology (DC_CL:0000043)(PMID:19243617).
Kit and Sca1-positive hematopoietic stem cell
true
CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive.
CALOHA:TS-0448
FMA:86475
CD133-positive hematopoietic stem cell
cell
Cell markers are associated with human hematopoietic stem cells. Originally described in the dendritic cell ontology (DC_CL:0000035)(PMID:19243617).
CD34-positive, CD38-negative hematopoietic stem cell
true
A cell that is maintained or propagated in a controlled artificial environment for use in an investigation.
haendel
2012-01-12T09:58:38Z
cell
'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells.
cell in vitro
true
true
A connective tissue cell found in bone.
adiehl
2011-11-16T04:28:16Z
cell
bone cell
true
A hematopoietic stem cell capable of rapid replenishment of myeloerythroid progenitors and limited self renewal capability. This cell is Kit-positive, Sca1-positive, CD34-positive, CD150-positive, and is Flt3-negative.
tmeehan
2010-01-08T09:19:25Z
ST stem cell
ST-HSC
cell
Markers are associated with mouse cells. These cells are also reportedly CD11b-low and CD90-low.
short term hematopoietic stem cell
true
A hematopoietic stem cell with long term self renewal capability. This cell is Kit-positive, Sca1-positive, CD150-positive, CD90-low, CD34-negative and Flt3-negative.
tmeehan
2010-01-08T09:19:28Z
LT stem cell
LT-HSC
cell
Markers are associated with mouse cells.
long term hematopoietic stem cell
true
An epithelial cell derived from endoderm.
tmeehan
2010-06-29T03:38:14Z
FMA:69075
cell
endo-epithelial cell
true
true
An epithelial cell derived from ectoderm.
tmeehan
2010-06-29T03:38:22Z
FMA:69074
cell
ecto-epithelial cell
true
true
Epithelial cell derived from mesoderm or mesenchyme.
tmeehan
2010-06-29T03:49:14Z
FMA:69076
epithelial mesenchymal cell
cell
meso-epithelial cell
true
true
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
MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense.
bone marrow cell
true
Epithelial cells derived from general body ectoderm and ectoderm placodes.
tmeehan
2010-08-26T08:31:08Z
FMA:70556
cell
general ecto-epithelial cell
true
An epithelial cell found in the lining of the stomach.
tmeehan
2010-08-25T03:22:08Z
CL:1000399
FMA:62948
cell
epithelial cell of stomach
true
A mucous cell in the epithelium of the stomach.
tmeehan
2010-08-25T03:38:51Z
CL:1000404
FMA:63464
cell
mucous cell of stomach
true
A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit.
tmeehan
2010-08-25T03:57:08Z
CL:1000400
FMA:62953
cell
stem cell of gastric gland
true
true
true
A basally situated, mitotically active, columnar-shaped keratinocyte attached to the basement membrane.
tmeehan
2010-08-26T03:12:49Z
CL:1000439
FMA:70571
cell
basal cell of epidermis
true
true
true
A stem cell that can give rise to the cells of the liver.
tmeehan
2010-08-30T02:00:42Z
FMA:86577
cell
hepatic stem cell
true
A transient hepatic stem cell observed after liver injury with a high nuclear to cytoplasm ratio that can differentiate into mature hepatocytes and bile duct cells. Arises from more than one tissue.
tmeehan
2010-08-30T02:01:49Z
CL:1000036
BTO:0004270
FMA:86576
hepatic oval cell
cell
hepatic oval stem cell
true
An epithelial cell of the tracheobronchial tree.
tmeehan
2010-09-02T02:09:14Z
CL:1000407
FMA:66816
cell
epithelial cell of tracheobronchial tree
true
An epithelial cell of the prostate.
tmeehan
2010-09-07T01:49:29Z
CL:1000295
CL:1000408
FMA:256163
FMA:66817
prostate epithelial cell
cell
epithelial cell of prostate
true
A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells).
tmeehan
2010-09-07T03:57:09Z
BTO:0002669
FMA:86711
PBSC
cell
peripheral blood stem cell
true
true
A pluripotent stem cell has the ability to form cells from all three germ layers (ectoderm, mesoderm, and endoderm). However, unlike totipotent stem cells, they cell can not generate all the cells of the whole organism such as placenta.
tmeehan
2010-09-07T04:26:06Z
FMA:70570
cell
pluripotent stem cell
true
A stem cell that can differentiate into a cardiac myocyte.
tmeehan
2010-09-07T04:40:32Z
FMA:75620
cell
primitive cardiac myocyte
true
true
A cell that is found in a zone occupying the bottom region of the crypt; provide the source of most of the cell types of the intestinal epithelium; proliferate by mitotic division; differentiates into columnar or goblet cells.
tmeehan
2010-09-08T09:21:22Z
FMA:63379
stem cell of intestinal crypt of Lieberkuhn
cell
intestinal crypt stem cell
true
true
An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus.
tmeehan
2010-09-08T09:26:53Z
cell
epithelial cell of alimentary canal
true
The stem cell from which glial precursor cell arises from.
tmeehan
2010-09-08T02:14:14Z
FMA:87171
totipotent neuroepithelial stem cell
cell
neuroepithelial stem cell
true
A taste receptor cell that is characterized by morphologically identifiable synaptic contacts with the gustatory nerve fibers and expression of the synaptic membrane protein-25 (SNAP-25) and NCAM.
tmeehan
2010-09-13T10:57:21Z
taste bud basal cell
FMA:67940
type 3 taste cell
cell
type III taste bud cell
true
true
A rounded, mitotically active stem cell which is the source of new cells of the taste bud; located basally.
tmeehan
2010-09-13T10:57:29Z
taste bud basal cell
FMA:62380
type 4 taste cell
cell
There is debate about the exact lineage of these cell types from this progenitor. See PMID:15738192.
type IV taste receptor cell
true
true
A cell that is part of the nervous system.
tmeehan
2010-09-15T01:34:57Z
CALOHA:TS-2040
FMA:70333
cell
neural cell
true
true
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
connective tissue cell
true
true
A cell of the embryo.
tmeehan
2010-09-15T03:39:21Z
CALOHA:TS-0263
FMA:82840
FMA:82841
WBbt:0007028
cell
embryonic cell
true
A stem cell of embryonic origin.
tmeehan
2010-09-15T03:44:35Z
BTO:0001086
CALOHA:TS-0263
FMA:82841
ESC
cell
This is an in vitro cell type and may be removed in future releases. These cells are reportedly SSEA-4-positive, CD73-negative, and CD324-positive.
embryonic stem cell
true
true
A cell of a fetus which is suspended in the amniotic fluid. Amniocytes are considered to arise from several tissues including fetal skin, the fetal urinary tract, umbilical cord, and the inner amniotic surface.
tmeehan
2010-09-20T10:13:37Z
BTO:0000066
cell
amniocyte
true
An epithelial cell of the bronchus.
tmeehan
2010-09-20T02:00:00Z
BTO:0002922
cell
bronchial epithelial cell
true
An epithelial cell type that lacks the columnar shape typical for other respiratory epithelial cells. This cell type is able to differentiate into other respiratory epithelial cells in response to injury.
tmeehan
2010-09-20T02:10:36Z
cell
basal epithelial cell of tracheobronchial tree
true
A stem cell located in the bulge of the hair follicle that can give rise to regenerate the new follicle with each hair cycle and to reepithelialize the epidermis during wound repair.
tmeehan
2010-09-20T03:07:03Z
bulge keratinocyte
cell
keratinocyte stem cell
true
true
A prostate epithelial cell that is CD133-positive, CD44-positive, integrin A2beta3-high. This cell is a stem cell for the prostate epithelium.
tmeehan
2010-09-20T03:21:06Z
CD133-positive prostate epithelial cell
cell
prostate stem cell
true
true
An undifferentiated cell of the prostate epithelium that lacks secretory activity.
tmeehan
2010-09-20T03:34:10Z
cell
basal cell of prostate epithelium
true
A multi-fate stem cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1.
tmeehan
2010-09-21T04:41:06Z
pancreatic endocrine progenitor
pancreatic islet progenitor cell
cell
progenitor cell of endocrine pancreas
true
A hematopoietic stem cell that exists during embryogenesis.
tmeehan
2010-09-22T09:05:13Z
cell
gestational hematopoietic stem cell
true
A hematopoietic stem cell that resides in the fetal liver. In mice, this cell type is first observed at E10.5. This cell type is MHC-positive, HSA-positive, AA4.1-positive, CD45-positive, Sca-1 positive, CD150-positive, CD48-negative and CD244-negative.
tmeehan
2010-09-22T09:08:32Z
cell
fetal liver hematopoietic progenitor cell
true
A hematopoietic stem found in the yolk sac. In mice, this cell type is Sca-1-negative, CD45-negative, MHC-negative, HSA-positive, AA4.1-positive, CD44-positive.
tmeehan
2010-09-22T09:08:34Z
hemangioblast precursor
cell
yolk sac hematopoietic stem cell
true
true
A hematopoietic stem cell of the placenta. This cell type is first observed E10.5 This cell type may give rise to fetal liver hematopoietic stem cells.
tmeehan
2010-09-22T10:30:02Z
cell
placental hematopoietic stem cell
true
A hematopoietic stem cell from the aorta-gonad-mesonephros region of the developing embryo. First seen at E10.5 in mouse embryos. May give rise to fetal liver HSC.
tmeehan
2010-09-22T10:31:49Z
cell
AGM hematopoietic stem cell
true
A cell located in the outermost proliferative zone of the external germinal layer that can differentiate into astroglial cells and granule cells. This cell type is glial fibrillary acidic protein-positive and NK1-positive.
tmeehan
2010-09-22T01:40:44Z
cell
granule cell precursor
true
An endo-epithelial cell of the respiratory tract.
tmeehan
2010-09-23T04:38:49Z
BTO:0004533
airway epithelial cell
cell
respiratory epithelial cell
true
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
somatic cell
true
A multi-fate stem cell that is the source of cells for growth of the mammary gland during puberty and gestation. This cell type gives rise to both the luminal and myoepithelial cell types of the gland, and have been shown to have the ability to regenerate the entire organ in mice. This cell type also plays an important role in carcinogenesis of the breast. This cell type is Lin-, CD24-positive, CD29-hi.
tmeehan
2010-11-10T01:46:51Z
cell
mammary stem cell
true
A mesenchymal stem cell of the amnion membrane.
tmeehan
2011-02-28T12:44:24Z
amniotic membrane stem cell
cell
amnion mesenchymal stem cell
true
A mesenchymal stem cell that is part of the bone marrow.
tmeehan
2011-02-28T01:47:47Z
cell
mesenchymal stem cell of the bone marrow
true
true
A mesenchymal stem cell of the chorionic membrane.
tmeehan
2011-02-28T03:04:35Z
cell
chorionic membrane mesenchymal stem cell
true
An epithelial cell of the intestine.
tmeehan
2011-03-01T05:18:31Z
cell
intestinal epithelial cell
true
A mesenchymal stem cell that is part of Wharton's jelly.
tmeehan
2011-03-01T09:51:18Z
cell
mesenchymal stem cell of Wharton's jelly
true
A mesenchymal stem cell of the umbilical cord.
tmeehan
2011-03-01T09:55:12Z
cell
mesenchymal stem cell of umbilical cord
true
true
A mesenchymal stem cell of adipose tissue.
tmeehan
2011-03-01T09:57:17Z
cell
mesenchymal stem cell of adipose
true
A mesenchymal stem cell of liver.
tmeehan
2011-03-01T09:58:51Z
cell
hepatic mesenchymal stem cell
true
true
A mesenchymal stem cell of the vertebrae.
tmeehan
2011-03-01T10:40:27Z
cell
vertebral mesenchymal stem cell
true
true
A neural crest cell that gives rise to cells of the enteric nervous system.
tmeehan
2011-03-06T07:24:35Z
cell
migratory enteric neural crest cell
true
An adult angioblastic cell released from the bone marrow, capable of blood circulation and participation in angiogenesis by differentiating into blood vessel endothelial cells. Their existence is controversial.
tmeehan
2011-03-14T12:11:18Z
EPC
cell
adult endothelial progenitor cell
true
tmeehan
2011-06-21T12:29:31Z
cell
epithelial cell of lower respiratory tract
true
A basal cell in the respiratory tract.
tmeehan
2011-06-21T03:11:10Z
airway basal cell
airway basal stem cell
cell
respiratory basal cell
true
true
A respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole. This cell types gives rise to alveolar cell types and Clara cells in response to lung injury. This cell type expresses markers Scgb1a1 and Sftpc.
tmeehan
2011-06-21T03:26:08Z
BASC
basal epithelial cell of bronchioalveolar duct junction
cell
bronchioalveolar stem cell
true
true
An amniotic stem cell is a mesenchymalstem cell extracted from amniotic fluid. Amniotic stem cells are able to differentiate into various tissue type such as skin, cartilage, cardiac tissue, nerves, muscle, and bone
tmeehan
2011-06-21T03:55:39Z
cell
Not clear to me if amniotic stem cell is a different cell type from amnion mesenchymal stem cells. They are treated as distinct in the literature as isolations methods are different, so I will keep them as separate terms for now.
amniotic stem cell
true
true
An epithelial fate stem cell derived form the amnion membrane.
tmeehan
2011-06-21T04:06:17Z
cell
amniotic epithelial stem cell
true
A glandular epithelial cell that is part of the stomach.
tmeehan
2011-07-11T01:20:35Z
CALOHA:TS-1284
FMA:86554
cell
glandular cell of stomach
true
true
A stem cell that can give rise to multiple cell types (i.e. smooth muscle, endothelial) in the developing heart.
tmeehan
2011-07-11T03:15:38Z
cell
Discrepancy in develops from origins prevents me from making the assertion that cardioblasts give rise to all instances of cardiocytes as we state cardiac muscle cells develop from cardiac myoblast, which in turn develop from muscle stem cell.
cardioblast
true
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
retinal progenitor cell
true
A neuroblast derived from a neural crest cell.
tmeehan
2011-08-22T09:24:15Z
cell
neural crest derived neuroblast
true
Lymphatic progenitor cells.
Ceri
2012-01-12T04:44:34Z
cell
Usually express Prox1, or prox1b.
lymphangioblast
true
Mesenchymal derived lymphatic progenitor cells that give rise to the superficial lymphatics.
Ceri
2012-01-12T05:01:22Z
cell
mesenchymal lymphangioblast
true
true
Lymphatic progenitor cells, derived from the veins, that give rise to lymphatic endothelial cells.
Ceri
2012-01-12T05:21:09Z
parachordal lymphangioblast
cell
vascular lymphangioblast
true
Multi fate stem cell that gives rise to to both hepatocytes and cholangiocytes as descendants.
hepatoblast
true
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
premigratory neural crest cell
true
Any hematopoietic cell that is a precursor of some other hematopoietic cell type.
hematopoietic precursor cell
true
A skeletal muscle satellite cell that divides by stem cell division. A proportion of this population undergoes symmetric stem cell division, producing two skeletal muscle satellite stem cells. The rest undergo asymmetric stem cell division - retaining their identity while budding off a daughter cell that differentiates into an adult skeletal muscle myoblast.
cell
skeletal muscle satellite stem cell
true
true
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
neural crest cell
true
true
A cell that, by division or terminal differentiation, can give rise to other cell types.
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
true
forebrain neuroblast
true
cell
stratified keratinized epithelial stem cell
true
cell
stratified non keratinized epithelial stem cell
true
A basal cell that is part of the epithelium of trachea.
FMA:263118
cell
basal cell of epithelium of trachea
true
true
A basal cell found in the bronchus epithelium.
CL:0002331
FMA:263120
basal cell of bronchus
cell
basal cell of epithelium of bronchus
true
true
true
A basal cell that is part of the epithelium of terminal bronchiole.
FMA:263122
cell
basal cell of epithelium of terminal bronchiole
true
A basal cell that is part of the epithelium of respiratory bronchiole.
FMA:263124
cell
basal cell of epithelium of respiratory bronchiole
true
A basal cell that is part of the epithelium of bronchiole.
FMA:263126
cell
basal cell of epithelium of lobular bronchiole
true
true
A somatic stem cell that is part of the epidermis.
FMA:70541
epidermal stem cell
cell
stem cell of epidermis
true
A basal cell that is part of the epithelium of esophagus.
FMA:70731
basal cell of esophageal epithelium
cell
epithelial cell of stratum germinativum of esophagus
true
A basal cell that is part of the urothelium.
FMA:84150
cell
basal cell of urothelium
true
a respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole, which gives rise to alveolar cell types and Clara cells in response to lung injury.
cl
bronchioalveolar stem cells
true
Any basal cell of epidermis that is part of a limb.
TermGenie
2014-06-25T02:28:25Z
cell
CL:2000033
limb basal cell of epidermis
true
Any mesenchymal stem cell that is part of a placenta.
TermGenie
2014-10-07T17:51:11Z
cell
CL:2000061
http://www.sciencellonline.com/site/productInformation.php?keyword=7140
placental amniotic mesenchymal stromal cell
true
Any migratory neural crest cell that is part of a cardiac neural crest.
TermGenie
2014-11-05T01:18:43Z
cell
CL:2000073
migratory cardiac neural crest cell
true
Any mesenchymal stem cell of the bone marrow that is part of a femur.
TermGenie
2014-12-02T19:07:31Z
cell
CL:2000079
mesenchymal stem cell of femoral bone marrow
true
Any mesenchymal stem cell of adipose that is part of a abdomen.
TermGenie
2014-12-02T19:10:34Z
cell
CL:2000080
mesenchymal stem cell of abdominal adipose
true
Any hair follicle dermal papilla cell that is part of a scalp.
TermGenie
2014-12-02T19:10:50Z
cell
CL:2000083
hair follicle dermal papilla cell of scalp
true
Any hematopoietic stem cell that is part of a umbilical cord blood.
TermGenie
2015-05-26T18:58:34Z
cell
CL:2000095
cord blood hematopoietic stem cell
true
true
spinal muscular atrophy
ICD9CM_2010:335.1
ICD9CM_2010:335.10
MSH2010_2010_02_22:D009134
SNOMEDCT_2010_1_31:192885003
SNOMEDCT_2010_1_31:192887006
SNOMEDCT_2010_1_31:5262007
UMLS_CUI:C0026847
URI: http://www.ebi.ac.uk/cellline#spinal_muscular_atrophy
true
true
"degenerative disease" EXACT [NCI2004_11_17:C27090]
"degenerative disorder (disorder)" EXACT [SNOMEDCT_2005_07_31:362975008]
"A disease of biological process that results_in the progressive deterioration of tissue or organ function or structure, whether due to normal bodily wear or lifestyle choices." [url:http\://en.wikipedia.org/wiki/Degenerative_disease]
degenerative disease
NCI2009_04D:C27090
SNOMEDCT_2010_1_31:362975008
UMLS_CUI:C1285162
URI: http://www.ebi.ac.uk/cellline#degenerative_disease
true
"HMN (Hereditary motor Neuropathy) Proximal type I" EXACT []
"Werdnig-Hoffman disease" EXACT [SNOMEDCT_2005_07_31:155016008]
"Werdnig-Hoffman disease" EXACT [SNOMEDCT_2005_07_31:267694009]
"Werdnig-Hoffmann disease (disorder)" EXACT [SNOMEDCT_2005_07_31:64383006]
"Werdnig-Hoffmann disease" EXACT [ICD9CM_2006:335.0]
"infantile muscular atrophy" EXACT [CSP2005:2057-3620]
"progressive muscular atrophy of infancy" EXACT [MTHICD9_2006:335.0]
hereditary motor neuropathy proximal type I
ICD9CM_2010:335.0
OMIM2009_05_01:253300
SNOMEDCT_2010_1_31:155016008
SNOMEDCT_2010_1_31:267694009
SNOMEDCT_2010_1_31:64383006
UMLS_CUI:C0043116
URI: http://www.ebi.ac.uk/cellline#hereditary_motor_neuropathy_proximal_type_I
true
A disease of anatomical entity that occurs in the muscular and/or skeletal system.
"Musculo-skeletal disorder NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:274149006]
"Musculo-skeletal disorder NOS" EXACT [SNOMEDCT_2005_07_31:156881000]
"Musculo-skeletal disorder NOS" EXACT [SNOMEDCT_2005_07_31:268142006]
"Musculoskeletal disease" EXACT [MTH:NOCODE]
"Musuloskeletal disease" EXACT [SNOMEDCT_2005_07_31:268047003]
"disorder of musculoskeletal system (disorder)" EXACT [SNOMEDCT_2005_07_31:928000]
"musculoskeletal disorder" EXACT [CSP2005:4000-0257]
MESH:D009140
NCI:C107377
SNOMEDCT_US_2016_03_01:156881000
SNOMEDCT_US_2016_03_01:268047003
SNOMEDCT_US_2016_03_01:268142006
SNOMEDCT_US_2016_03_01:274149006
SNOMEDCT_US_2016_03_01:928000
UMLS_CUI:C0026857
disease_ontology
DOID:17
musculoskeletal system disease
MSH2010_2010_02_22:D009140
SNOMEDCT_2010_1_31:156881000
SNOMEDCT_2010_1_31:268047003
SNOMEDCT_2010_1_31:268142006
SNOMEDCT_2010_1_31:274149006
SNOMEDCT_2010_1_31:928000
UMLS_CUI:C0026857
URI: http://www.ebi.ac.uk/cellline#musculoskeletal_system_disease
true
motor neuron disease
ICD9CM_2010:335.2
MSH2010_2010_02_22:D016472
SNOMEDCT_2010_1_31:155015007
SNOMEDCT_2010_1_31:192888001
SNOMEDCT_2010_1_31:192889009
SNOMEDCT_2010_1_31:192890000
SNOMEDCT_2010_1_31:37340000
UMLS_CUI:C0085084
URI: http://www.ebi.ac.uk/cellline#motor_neuron_disease
true
true
"myelopathy" RELATED []
spinal cord disease
ICD9CM_2010:336.9
MSH2010_2010_02_22:D013118
OMIM2009_05_01:MTHU005441
SNOMEDCT_2010_1_31:155020007
SNOMEDCT_2010_1_31:192908002
SNOMEDCT_2010_1_31:192913003
SNOMEDCT_2010_1_31:267587000
SNOMEDCT_2010_1_31:267695005
SNOMEDCT_2010_1_31:48522003
SNOMEDCT_2010_1_31:95648003
UMLS_CUI:C0037928
URI: http://www.ebi.ac.uk/cellline#spinal_cord_disease
true
"A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system." [url:http\://en.wikipedia.org/wiki/Central_nervous_system_disease]
central nervous system disease
MSH2010_2010_02_22:D002493
NCI2009_04D:C2934
SNOMEDCT_2010_1_31:138748005
SNOMEDCT_2010_1_31:154981003
SNOMEDCT_2010_1_31:155049004
SNOMEDCT_2010_1_31:155059003
SNOMEDCT_2010_1_31:192641002
SNOMEDCT_2010_1_31:193076009
SNOMEDCT_2010_1_31:194566008
SNOMEDCT_2010_1_31:23853001
SNOMEDCT_2010_1_31:267144009
SNOMEDCT_2010_1_31:267679005
SNOMEDCT_2010_1_31:267700003
SNOMEDCT_2010_1_31:267702006
SNOMEDCT_2010_1_31:275539005
UMLS_CUI:C0007682
URI: http://www.ebi.ac.uk/cellline#central_nervous_system_disease
true
"A disease that involves any biological process (GO:0008150) specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms." [DO:wk\,ls]
disease of biological process
URI: http://www.ebi.ac.uk/cellline#disease_of_biological_process
true
A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
MESH:D004194
NCI:C2991
SNOMEDCT_US_2016_03_01:64572001
UMLS_CUI:C0012634
disease_ontology
DOID:4
disease
true
tissue disease
URI: http://www.ebi.ac.uk/cellline#tissue_disease
true
neuromuscular disease
ICD9CM_2010:358
ICD9CM_2010:358.9
MSH2010_2010_02_22:D009468
SNOMEDCT_2010_1_31:1664005
SNOMEDCT_2010_1_31:193218007
SNOMEDCT_2010_1_31:255522009
SNOMEDCT_2010_1_31:257277002
UMLS_CUI:C0027868
URI: http://www.ebi.ac.uk/cellline#neuromuscular_disease
true
true
hereditary degenerative disease of central nervous system
SNOMEDCT_2010_1_31:192838009
SNOMEDCT_2010_1_31:192842007
UMLS_CUI:C0014887
URI: http://www.ebi.ac.uk/cellline#hereditary_degenerative_disease_of_central_nervous_system
true
true
anterior horn cell disease
ICD9CM_2010:335
ICD9CM_2010:335.9
SNOMEDCT_2010_1_31:155014006
SNOMEDCT_2010_1_31:192884004
SNOMEDCT_2010_1_31:192892008
SNOMEDCT_2010_1_31:267693003
SNOMEDCT_2010_1_31:85672005
UMLS_CUI:C0154681
URI: http://www.ebi.ac.uk/cellline#anterior_horn_cell_disease
true
"Neurodegenerative disease" EXACT [NCI2004_11_17:C4802]
"A degenerative disease that results_in the progressive loss of structure or function of neurons, including death of neurons." [url:http\://en.wikipedia.org/wiki/Neurodegeneration]
neurodegenerative disease
MSH2010_2010_02_22:D019636
NCI2009_04D:C4802
UMLS_CUI:C0524851
URI: http://www.ebi.ac.uk/cellline#neurodegenerative_disease
true
true
muscle tissue disease
URI: http://www.ebi.ac.uk/cellline#muscle_tissue_disease
true
A disease that manifests in a defined anatomical structure.
"acellular anatomical structure disease" EXACT []
"disease of anatomical set" EXACT []
"disease of anatomical structure" EXACT []
"disease of material anatomical entity" EXACT []
"disease of physical anatomical entity" EXACT []
"disease of set of heterogenous clusters" EXACT []
DOID:1
DOID:2
DOID:5
DOID:71
DOID:72
DOID:8
disease_ontology
DOID:7
"A disease that manifests in a defined anatomical structure." [DO:wk\,ls, URL:http\://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=anatomic]
disease of anatomical entity
URI: http://www.ebi.ac.uk/cellline#disease_of_anatomical_entity
true
true
nervous system disease
ICD9CM_2010:349.9
MSH2010_2010_02_22:D009422
NCI2009_04D:C26835
SNOMEDCT_2010_1_31:118940003
SNOMEDCT_2010_1_31:154981003
SNOMEDCT_2010_1_31:155262005
SNOMEDCT_2010_1_31:192641002
SNOMEDCT_2010_1_31:267679005
SNOMEDCT_2010_1_31:286946008
UMLS_CUI:C0027765
URI: http://www.ebi.ac.uk/cellline#nervous_system_disease
true
"Neuropathy (disorder)" EXACT [SNOMEDCT_2005_07_31:264554005]
"Neuropathy (disorder)" EXACT [SNOMEDCT_2005_07_31:386033004]
"Neuropathy" EXACT [MTH:NOCODE]
"Neuropathy" EXACT [SNOMEDCT_2005_07_31:193167000]
"Neuropathy" EXACT [SNOMEDCT_2005_07_31:277317008]
"Neuropathy" EXACT [SNOMEDCT_2005_07_31:277878001]
"Neuropathy, NOS" EXACT [SNOMEDCT_2005_07_31:42658009]
neuropathy
NCI2009_04D:C4731
OMIM2009_05_01:MTHU016030
SNOMEDCT_2010_1_31:193167000
SNOMEDCT_2010_1_31:264554005
SNOMEDCT_2010_1_31:277317008
SNOMEDCT_2010_1_31:277878001
SNOMEDCT_2010_1_31:386033004
SNOMEDCT_2010_1_31:42658009
UMLS_CUI:C0442874
URI: http://www.ebi.ac.uk/cellline#neuropathy
true
osteoblast differentiation
true
hematopoietic progenitor cell differentiation
true
immune system process
true
production of molecular mediator of immune response
true
regulation of immune system process
true
positive regulation of immune system process
true
true
regulation of leukocyte migration
true
true
positive regulation of leukocyte migration
true
true
true
regulation of leukocyte chemotaxis
true
true
positive regulation of leukocyte chemotaxis
true
true
true
antimicrobial peptide production
true
antimicrobial peptide secretion
true
peptide secretion
true
true
developmental process involved in reproduction
true
true
system process
true
cellular_component
true
cell
true
true
transport
true
movement of cell or subcellular component
true
gamete generation
true
germ cell development
true
true
true
spermatogenesis
true
female gamete generation
true
biological_process
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
GO:0000004
GO:0007582
Wikipedia:Biological_process
biological process
physiological process
biological_process
GO:0008150
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
biological_process
true
detection of chemical stimulus
true
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GO:0008151
GO:0050875
cell physiology
cellular physiological process
cell growth and/or maintenance
biological_process
GO:0009987
cellular process
true
peptide transport
true
true
cell migration
true
stem cell division
true
transmission of nerve impulse
true
true
cellular process involved in reproduction in multicellular organism
true
true
reproductive process
true
signaling
true
cell differentiation
true
neuron differentiation
true
regulation of cell migration
true
positive regulation of cell migration
true
true
epithelial cell differentiation
true
regulation of response to external stimulus
true
positive regulation of response to external stimulus
true
true
multicellular organismal process
true
developmental process
true
regulation of localization
true
secretion by cell
true
true
macromolecular complex
true
cardiocyte differentiation
true
multicellular organismal signaling
true
true
Self-propelled movement of a cell or organism from one location to another.
biological_process
GO:0040011
locomotion
true
regulation of locomotion
true
positive regulation of locomotion
true
true
MHC protein complex
true
MHC class II protein complex
true
muscle cell differentiation
true
amide transport
true
protein complex
true
membrane part
true
plasma membrane part
true
true
cell part
cell part
true
true
fat cell differentiation
true
secretion
true
somatic stem cell division
true
male gamete generation
true
cell development
true
true
oogenesis
true
true
positive regulation of biological process
true
positive regulation of cellular process
true
true
regulation of response to stimulus
true
positive regulation of response to stimulus
true
true
multicellular organismal reproductive process
true
anatomical structure development
true
cellular developmental process
true
true
cell motility
true
true
regulation of biological process
true
regulation of cellular process
true
nervous system process
true
response to stimulus
true
detection of stimulus involved in sensory perception
true
detection of chemical stimulus involved in sensory perception
true
true
detection of chemical stimulus involved in sensory perception of taste
true
regulation of chemotaxis
true
true
positive regulation of chemotaxis
true
true
true
striated muscle cell differentiation
true
localization
true
establishment of localization
true
regulation of cellular component movement
true
true
positive regulation of cellular component movement
true
true
cell division
true
detection of stimulus
true
cardiac muscle cell differentiation
true
true
chondroblast differentiation
true
biological regulation
true
regulation of granulocyte chemotaxis
true
positive regulation of granulocyte chemotaxis
true
true
organic substance transport
true
nitrogen compound transport
true
regulation of neutrophil chemotaxis
true
true
positive regulation of neutrophil chemotaxis
true
true
true
membrane protein complex
true
true
plasma membrane protein complex
true
true
regulation of neutrophil migration
true
positive regulation of neutrophil migration
true
true
regulation of cell motility
true
true
positive regulation of cell motility
true
true
true
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was
proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and
Cristian Cocos, and subsequently moved to IAO where the objective for
which the original term was defined was satisfied with the definition
of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
measurement unit label
true
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Alan Ruttenberg
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
OBI_0000217
objective specification
true
action specification
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
Alan Ruttenberg
OBI Plan and Planned Process branch
action specification
true
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n
GROUP: IAO
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
datum label
true
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some
information-like stuff that might be put into a computer and that is
meant, by someone, to denote and/or to be interpreted by some
process... I would include lists, tables, sentences... I think I might
defer to Barry, or to Brian Cantwell Smith
JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
data item
true
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).
Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
PERSON: Chris Stoeckert
OBI_0000142
information content entity
information content entity
true
1
1
10 feet. 3 ml.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in
this case we explicitly refer to the singular form
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
scalar measurement datum
true
directive information entity
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
directive information entity
true
graph
A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
PERSON: Lawrence Hunter
person:Alan Ruttenberg
person:Allyson Lister
OBI_0000240
group:OBI
graph
true
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
OBI_0000270
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
algorithm
true
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
curation status specification
true
data about an ontology part
data about an ontology part is a data item about a part of an ontology, for example a term
Person:Alan Ruttenberg
data about an ontology part
true
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Alan Ruttenberg
OBI Plan and Planned Process branch
OBI_0000344
2/3/2009 Comment from OBI review.
Action specification not well enough specified.
Conditional specification not well enough specified.
Question whether all plan specifications have objective specifications.
Request that IAO either clarify these or change definitions not to use them
plan specification
true
measurement datum
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
person:Chris Stoeckert
OBI_0000305
group:OBI
measurement datum
true
material information bearer
A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
a brain
a hard drive
A material entity in which a concretization of an information content entity inheres.
GROUP: IAO
material information bearer
true
figure
Any picture, diagram or table
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
PERSON: Lawrence Hunter
figure
true
diagram
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
A figure that expresses one or more propositions
PERSON: Lawrence Hunter
diagram
true
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
PERSON: Lawrence Hunter
document
true
A scalar measurement datum that is the result of measurement of length quality
Alan Ruttenberg
length measurement datum
true
A scalar measurement datum that is the result of measurement of mass quality
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
Person:Alan Ruttenberg
mass measurement datum
true
A scalar measurement datum that is the result of measuring a temporal interval
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
Person:Alan Ruttenberg
time measurement datum
true
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
a planned process in which a document is created or added to by including the specified input in it.
6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
Bjoern Peters
wikipedia http://en.wikipedia.org/wiki/Documenting
documenting
true
line graph
A line graph is a type of graph created by connecting a series of data
points together with a line.
PERSON:Chris Stoeckert
PERSON:Melanie Courtot
line chart
GROUP:OBI
WEB: http://en.wikipedia.org/wiki/Line_chart
line graph
true
time stamped measurement datum
true
a document that denotes some identity and is concretized by the bearer of some credential role
Amanda Hicks
identity document
true
a documented identity is the aggregate of all data items about an entity. Notice that a documented identity is not itself a document since a document is intended to be understood as a whole and data items about an individual are usually scattered across different documents.
Amanda Hicks
is an aggregate of ICEs also an ICE? yes
Is part_of the appropriate relation to use for data items and documented identities?
documented identity
true
I order a beer and the bartender authenticates my age by looking at my DOB on my driver's license. I sign into my email account, and the system authenticates my permission to read the email by checking the password I enter against my password listed in the database.
Authentication is the act of checking or verifying an identity claim (that is either tacit or explicit).
Amanda Hicks
authentication
true
a role that inheres in a concretization of an identity document and is realized by an authentication process
Amanda Hicks
credential role
true
Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom
A process that is carried out by a conscious being or an aggregate of conscious beings and is spontaneous, directed towards other conscious beings and aggregates thereof and needs to be perceived.
Mathias Brochhausen
MB: Regarding the use of the term 'sponteneous' in the definition:
The term is used in the following meaning of being self generated. It does not stand in contrast to being planned.
social act
true
Muridae
Muridae
true
Mus musculus
"Mus muscaris" RELATED misnomer []
"house mouse" EXACT genbank_common_name []
"mice C57BL/6xCBA/CaJ hybrid" RELATED misspelling []
"mouse" EXACT common_name []
house mouse
mouse
Mus musculus
GC_ID:1
URI: http://www.ebi.ac.uk/cellline#Mus_musculus
true
Viruses
Viruses
true
Euteleostomi
bony vertebrates
Euteleostomi
true
true
Bacteria
eubacteria
Bacteria
true
Homininae
Homininae
true
Archaea
Archaea
true
Eukaryota
eucaryotes
eukaryotes
GC_ID:1
PMID:23020233
eucaryotes
eukaryotes
ncbi_taxonomy
Eucarya
Eucaryotae
Eukarya
Eukaryotae
eukaryotes
Eukaryota
true
Euarchontoglires
Euarchontoglires
true
true
Glires
"Rodents and rabbits" EXACT genbank_common_name []
Rodents and rabbits
Glires
GC_ID:1
URI: http://www.ebi.ac.uk/cellline#Glires
true
Simiiformes
Simiiformes
true
Hominoidea
"ape" EXACT common_name []
"apes" EXACT common_name []
ape
apes
Hominoidea
GC_ID:1
URI: http://www.ebi.ac.uk/cellline#Hominoidea
true
Tetrapoda
tetrapods
Tetrapoda
true
Amniota
amniotes
Amniota
true
Theria <Mammalia>
Theria
Theria <Mammalia>
true
Opisthokonta
Opisthokonta
true
Bilateria
Bilateria
true
Sciurognathi
Sciurognathi
true
Muroidea
Muroidea
true
Murinae
Murinae
true
Mammalia
"mammals" EXACT genbank_common_name []
"mammals" RELATED blast_name []
mammals
Mammalia
GC_ID:1
URI: http://www.ebi.ac.uk/cellline#Mammalia
true
Vertebrata <Metazoa>
Vertebrata
vertebrates
Vertebrata <Metazoa>
true
Craniata <chordata>
Craniata
Craniata <chordata>
true
Eutheria
eutherian mammals
placental mammals
placentals
Eutheria
true
Primates
"Primata" RELATED synonym []
"primate" EXACT equivalent_name []
"primates" RELATED blast_name []
primate
Primates
GC_ID:1
URI: http://www.ebi.ac.uk/cellline#Primates
true
Catarrhini
Catarrhini
true
Hominidae
"Pongidae" RELATED synonym []
"great apes" EXACT common_name []
great apes
Hominidae
GC_ID:1
URI: http://www.ebi.ac.uk/cellline#Hominidae
true
Homo sapiens
Homo sapiens
"human" EXACT genbank_common_name []
human
human being
man
GC_ID:1
human
man
ncbi_taxonomy
Homo sapiens
Homo sapiens
GC_ID:1
URI: http://www.ebi.ac.uk/cellline#Homo_sapiens
true
Rodentia
"rodents" EXACT genbank_common_name []
"rodents" RELATED blast_name []
rodents
Rodentia
GC_ID:1
URI: http://www.ebi.ac.uk/cellline#Rodentia
true
A measurement of the number of cells per unit volume or area.
C120538
Quantitative Concept
Cell Density
C0162339
CDISC
A measurement of the number of cells contained in a unit of volume.
CELLDENS
Cell Density
Cell Density
true
A process in which blood or tissue samples are analyzed to determine their human leukocyte antigen (HLA) profiles.
C71329
Laboratory Procedure
HLA Typing
C0242318
HLA_Typing
HLA Testing
HLA Typing
HLA Typing
true
fluorescent reporter intensity
A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.
person:Chris Stoeckert
group:OBI
From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem.
fluorescent reporter intensity
true
planned process
planned process
Injecting mice with a vaccine in order to test its efficacy
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some
objectives is a planned process.
Bjoern Peters
branch derived
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
planned process
planned process
true
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
PERSON: Alan Ruttenberg
processed material
true
ratio of collected to emitted light
10%
A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role
person:Chris Stoeckert
person:Kevin Clancy
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
ratio of collected to emitted light
true
investigation
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
Bjoern Peters
OBI branch derived
Could add specific objective specification
Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core
editor = PRS
study
investigation
true
evaluant role
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
GROUP: Role Branch
OBI
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
evaluant role
true
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
PlanAndPlannedProcess Branch
measuring
scientific observation
OBI branch derived
study assay
any method
assay
true
culture medium
culture medium
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178
Modification made by JZ.
Person: Jennifer Fostel, Jie Zheng
OBI
culture medium
true
reagent role
Buffer, dye, a catalyst, a solvating agent.
A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
PERSON:Matthew Brush
reagent
PERSON:Matthew Brush
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
(copied from ReO)
Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique.
Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated.
In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
reagent role
true
material processing
material processing
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca Serra
material transformation
OBI branch derived
material processing
true
measured expression level
Examples are quantified data from an expression microarray experiment, PCR measurements, etc.
A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts.
person:Chris Stoeckert
OBI Data Transformation branch
measured expression level
true
specimen role
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
blood taken from animal: animal continues in study, whereas blood has role specimen.
something taken from study subject, leaves the study and becomes the specimen.
parasite example
- when parasite in people we study people, people are subjects and parasites are specimen
- when parasite extracted, they become subject in the following study
specimen can later be subject.
GROUP: Role Branch
OBI
specimen role
true
number of particles in subset
500, 200, 0
A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role
person:Kevin Clancy
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
number of particles in subset
true
number of lost events electronic
74, 0, 14 events lost due to data acquisition electronic coincidence.
A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role.
person:Kevin Clancy
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
number of lost events electronic
true
parameter threshold
0.01, 0.03
A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role
person:Kevin Clancy
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
parameter threshold
true
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based:
1) there are organization_member_roles (president, treasurer, branch
editor), with individual persons as bearers
2) there are organization_roles (employer, owner, vendor, patent holder)
3) an organization has a charter / rules / bylaws, which specify what roles
there are, how they should be realized, and how to modify the
charter/rules/bylaws themselves.
It is debatable what the organization itself is (some kind of dependent
continuant or an aggregate of people). This also determines who/what the
bearer of organization_roles' are. My personal favorite is still to define
organization as a kind of 'legal entity', but thinking it through leads to
all kinds of questions that are clearly outside the scope of OBI.
Interestingly enough, it does not seem to matter much where we place
organization itself, as long as we can subclass it (University, Corporation,
Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,
W3C, University of Oklahoma), and have it play roles.
This leads to my proposal: We define organization through the statements 1 -
3 above, but without an 'is a' statement for now. We can leave it in its
current place in the is_a hierarchy (material entity) or move it up to
'continuant'. We leave further clarifications to BFO, and close this issue
for now.
James Malone
Jie Zheng
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Philippe Rocca-Serra
PERSON: Susanna Sansone
Tomasz Adamusiak
organisation
GROUP: OBI
MO_177
An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
organization
organization
EFO_URI: http://www.ebi.ac.uk/efo/EFO_0002010
true
number of lost events computer
0, 125, 787 events lost due to computer busy.
A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role
person:Kevin Clancy
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
number of lost events computer
true
protocol
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
PlanAndPlannedProcess Branch
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
study protocol
protocol
true
analyte role
Glucose in blood (measured in an assay to determine the concentration of glucose).
A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
qualities such as weight, color are not assayed but measured, so they do not fall into this category.
GROUP: Role Branch
OBI
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
analyte role
true
material to be added role
drug added to a buffer contained in a tube; substance injected into an animal;
material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
Role Branch
OBI
9 March 09 from discussion with PA branch
material to be added role
true
interpreting data
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
Bjoern Peters
drawing a conclusion based on data
true
planning
The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
a process of creating or modifying a plan specification
7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
Bjoern Peters
Bjoern Peters
Plans and Planned Processes Branch
planning
true
information processor function
An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process.
Frank Gibson
data processor function
information processor function
true
analyte measurement objective
The objective to measure the concentration of glucose in a blood sample
an assay objective to determine the presence or concentration of an analyte in the evaluant
PERSON: Bjoern Peters
PPPB branch
analyte measurement objective
true
assay objective
the objective to determine the weight of a mouse.
an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
PPPB branch
PPPB branch
assay objective
true
analyte assay
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
2013-09-23: simplify equivalent axiom
Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement.
logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum
and
('has measurement unit label' some 'measurement unit label') and
('is quality measurement of' some 'molecular concentration'))
PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg
PERSON:Bjoern Peters
PERSON:Helen Parkinson
PERSON:Philippe Rocca-Serra
PERSON:Alan Ruttenberg
GROUP:OBI Planned process branch
analyte assay
true
measure function
A glucometer measures blood glucose concentration, the glucometer has a measure function.
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
PERSON: Daniel Schober
PERSON: Helen Parkinson
PERSON: Melanie Courtot
PERSON:Frank Gibson
measure function
true
consume data function
Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data.
PERSON: Daniel Schober
PERSON: Frank Gibson
PERSON: Melanie Courtot
consume data function
true
material transformation objective
material transformation objective
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
artifact creation objective
GROUP: OBI PlanAndPlannedProcess Branch
material transformation objective
true
study design execution
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
a planned process that carries out a study design
removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
branch derived
6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
study design execution
true
material separation objective
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
is an objective to transform a material entity into spatially separated components.
PPPB branch
PPPB branch
material separation objective
true
specimen collection process
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
A planned process with the objective of collecting a specimen.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker:
http://sourceforge.net/p/obi/obi-terms/716/
Bjoern Peters
specimen collection
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
6/9/09: used at workshop
specimen collection process
true
portioning objective
The objective to obtain multiple aliquots of an enzyme preparation.
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
portioning objective
true
separation into different composition objective
The objective to obtain cells contained in a sample of blood.
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
separation into different composition objective
true
specimen collection objective
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification to obtain a material entity for potential use as an input during an investigation.
Bjoern Peters
Bjoern Peters
specimen collection objective
true
survival rate
A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring.
Oliver He
adapted from wikipedia
http://en.wikipedia.org/wiki/Survival_rate
survival rate
true
spike train datum
Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog
A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time.
needs more work to see exactly what the data set looks like - HP
Helen Parkinson, Alan Ruttenberg
spike train measurement
Jessica Turner, NIF
spike train datum
true
material maintenance objective
An objective specification maintains some or all of the qualities of a material over time.
PERSON: Bjoern Peters
PERSON: Bjoern Peters
material maintenance objective
true
primary structure of DNA macromolecule
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
placeholder for SO
BP et al
primary structure of DNA macromolecule
true
material maintenance
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
material maintenance
true
categorical measurement datum
A measurement datum that is reported on a categorical scale
Bjoern Peters
nominal mesurement datum
Bjoern Peters
categorical measurement datum
true
handedness assay
The Edinburgh handedness assay is a specific method of determing handedness
A handedness assay measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure.
Helen Parkinson
handedness test
http://en.wikipedia.org/wiki/Handedness
handedness assay
true
processed specimen
A tissue sample that has been sliced and stained for a histology study.
A blood specimen that has been centrifuged to obtain the white blood cells.
A specimen that has been intentionally physically modified.
Bjoern Peters
Bjoern Peters
A tissue sample that has been sliced and stained for a histology study.
processed specimen
true
true
categorical label
The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
Bjoern Peters
Bjoern Peters
categorical label
true
device
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform.
2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:
(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.
(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.
(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.
In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
PERSON: Helen Parkinson
instrument
OBI development call 2012-12-17.
device
true
1
scalar score from composite inputs
A measurement datum which is the result of combining multiple datum. For example, a mean or summary score.
JT: We included this because we wanted to talk about an output from a questionnaire that summarized the answers to the questionnaire, but which was not actually the answer to any single question.
Person: Jessica Turner
questionaire score
Person: Jessica Turner
JZ: can we defined it logically as the output of some data transformation, like aggragate data transformation?
scalar score from composite inputs
true
sequence data
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
Person:Chris Stoeckert
GROUP: OBI
sequence data
true
handedness categorical measurement datum
A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally
PERSON:Alan Ruttenberg
PERSON:Jessica Turner
handedness categorical measurement datum
true
dose
An organism has been injected 1ml of vaccine
A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
dose
true
1
Edinburgh score
A score that measures the dominance of a person's right or left hand in everyday activities.
Person: Alan Ruttenberg
Person:Jessica Turner
PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html
Edinburgh score
true
questionnaire
A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document.
JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
Need to clarify if this is a document or a directive information entity (or what their connection is))
PERSON: Jessica Turner
Merriam-Webster
questionnaire
true
Edinburgh handedness assay
The Edinburgh Handedness assay is an assay in which a set of questions = the Edinburgh Handedness inventory - is asked and the answers to these questions are turned into a score, used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand.
PERSON:Jessica Turner
Person:Alan Ruttenberg
WEB:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory
Edinburgh handedness assay
true
binding constant
The predicted or measured binding affinity of a peptide to a MHC molecule can be captured in the binding constants "IC50 = 12 nM" or "t 1/2 = 30 minutes".
A binding datum about the disposition of two or more material entities to form complexes which comes in the form of a scalar and unit that are utilized in equations that model the binding process
10/6/11 BP: The distinction between binding datum and binding constant is based on the later being part of an equation. That should be captured in the logical definition here, and used to make it to a defined class.
PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
binding constant
true
3D structural organization datum
The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR.
A measurement datum that describes the structural orientation of a material entity in 3D space.
PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters
3D structural organization datum
true
age since planting measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing.
PERSON:Chris Stoeckert, Jie Zheng
MO_495 planting
Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call.
Term proposed by Bjoern on Nov 8, 2010 dev call
Supported by Alan on Nov 15, 2010 dev call
age since planting measurement datum
true
age since hatching measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg.
PERSON:Chris Stoeckert, Jie Zheng
MO_745 hatching
age since hatching measurement datum
true
age measurement assay
An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is the beginning of some transitional state of the bearer such as birth or when planted.
This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature.
PERSON: Alan Ruttenberg
OBI group
age measurement assay
true
age since egg laying measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism.
PERSON:Chris Stoeckert, Jie Zheng
MO_767 egg laying
age since egg laying measurement datum
true
age since germination measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth.
Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance.
PERSON:Chris Stoeckert, Jie Zheng
MO_590 germination
age since germination measurement datum
true
age since eclosion measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon.
PERSON:Chris Stoeckert, Jie Zheng
MO_876 eclosion
age since eclosion measurement datum
true
age since sowing measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination.
PERSON:Chris Stoeckert, Jie Zheng
MO_748 sowing
age since sowing measurement datum
true
age since coitus measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction.
PERSON:Chris Stoeckert, Jie Zheng
MO_783 coitus
age since coitus measurement datum
true
age measurement datum
A time measurement datum that is the result of measurement of age of an organism
note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet.
life of bearer doesn't imply organism
this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature
age as a quality is dubious; we plan to revisit
stages in development are currently handled with controlled vocabulary, such as 2-somite stage
PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
MO_178 Age
In MageTab file, we use
initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.)
Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class
discussed on Nov 15, dev call
All subtype will be defined by textual definition now.
age measurement datum
true
age since fertilization measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote.
Definition of fertilization comes from GO.
PERSON:Chris Stoeckert, Jie Zheng
MO_701 fertilization
age since fertilization measurement datum
true
age since birth measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
PERSON:Chris Stoeckert, Jie Zheng
MO_710 birth
age since birth measurement datum
true
half life datum (t 1/2)
The time it takes for 50% of a class of stochastic processes to occur.
Bjoern Peters
t 1/2
Bjoern Peters
half life datum (t 1/2)
true
dose response curve
A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve.
Bjoern Peters; Randi Vita
dose response curve
true
half maximal effective concentration (EC50)
Determining the potentency of a drug / antibody / toxicant by measuring a graded dose response curve, and determining the concentration of the compound where 50% of its maximal effect is observed.
half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time.
Bjoern Peters; Randi Vita
wikipedia
half maximal effective concentration (EC50)
true
binding datum
A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is.
Bjoern Peters; Randi Vita
binding datum
true
half maximal inhibitory concentration (IC50)
Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited.
Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect.
Bjoern Peters; Randi Vita
wikipedia
half maximal inhibitory concentration (IC50)
true
sampling time measurement datum
A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
Person: Chris Stoeckert
time point
MO_738 timepoint
sampling time measurement datum
true
minimal inhibitory concentration
A scalar measurement datum that indicates the lowest concentration at which a specific compound significantly inhibits a process from occurring compared to in the absence of the compound.
Created following request by Albert Goldfain
PERSON:Bjoern Peters
Bjoern Peters, coordinated with Albert Goldfain
minimal inhibitory concentration
true
sequence assembly algorithm
An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured.
Person: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Assembly Algorithm
NIAID GSCID-BRC
sequence assembly algorithm
true
PDB file
The file found in the pdb with the identifier 3pe4
http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3pe4
A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned.
PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum
PDB file
true
equilibrium dissociation constant (KD)
KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb
A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate)
PERSON: Bjoern Peters, Randi Vita
IEDB
equilibrium dissociation constant (KD)
true
equilibrium association constant (KA)
KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens.
A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate)
PERSON: Bjoern Peters, Randi Vita
IEDB
equilibrium association constant (KA)
true
rate measurement datum
The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.
A scalar measurement datum that represents the number of events occuring over a time interval
PERSON: Bjoern Peters, Randi Vita
IEDB
rate measurement datum
true
equilibrium dissociation constant (KD) approximated by IC50
A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor.
PERSON: Bjoern Peters, Randi Vita
http://dx.doi.org/10.1016/0006-2952(73)90196-2
equilibrium dissociation constant (KD) approximated by IC50
true
true
DNA sequence data
The part of a FASTA file that contains the letters ACTGGGAA
A sequence data item that is about the primary structure of DNA
OBI call; Bjoern Peters
OBI call; Melanie Courtout
8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
DNA sequence data
true
equilibrium dissociation constant (KD) approximated by EC50
A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand.
PERSON: Bjoern Peters, Randi Vita
Assay Development: Fundamentals and Practices, By Ge Wu, page 74
equilibrium dissociation constant (KD) approximated by EC50
true
true
half life of binding datum
The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate.
A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association.
PERSON: Bjoern Peters, Randi Vita
IEDB
half life of binding datum
true
true
binding
A peptide binding to an MHC molecule to form a complex.
The process of material entities forming complexes.
9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point.
PERSON: Bjoern Peters, Randi Vita
IEDB
binding
true
PDB file chain
The 'D' chain in the PDB file 2BSE identifies the heavy chain of the antibody in the protein:antibody complex
A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities
PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum
IEDB
PDB file chain
true
binding off rate measurement datum (koff)
A rate measurement datum of how quickly bound complexes disassociate
PERSON: Bjoern Peters, Randi Vita
IEDB
binding off rate measurement datum (koff)
true
true
binding on rate measurement datum (kon)
A rate measurement datum of how quickly bound complexes form
PERSON: Bjoern Peters, Randi Vita
IEDB
binding on rate measurement datum (kon)
true
true
specimen collection time measurement datum
A time measurement datum that is the measure of the time when the specimens are collected.
Person: Chris Stoeckert, Jie Zheng
collection date
NIAID GSCID-BRC metadata working group
Specimen Collection Date
NIAID GSCID-BRC
specimen collection time measurement datum
true
latitude coordinate measurement datum
A measurement datum that is the measure of the latitude coordinate of a site.
Person: Chris Stoeckert, Jie Zheng
latitude
NIAID GSCID-BRC metadata working group
Specimen Collection Location - Latitude
NIAID GSCID-BRC
latitude coordinate measurement datum
true
longitude coordinate measurement datum
A measurement datum that is the measure of the longitude coordinate of a site.
Person: Chris Stoeckert, Jie Zheng
longitude
NIAID GSCID-BRC metadata working group
Specimen Collection Location - Longitude
NIAID GSCID-BRC
longitude coordinate measurement datum
true
secondary cultured cell
A cultured cell that has been passaged or derives from a cell that has been passaged in culture.
The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
Person: Matthew Brush
PERSON: Matthew Brush
A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture.
secondary cultured cell
true
establishing cell line
a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset).
2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time.
Person: Matthew Brush
PERSON:Matthew Brush
establishing cell line
true
sequence assembly process
A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs).
PRS/AGB:
changed to restrictions by adding 2 possible specified outputs (N50 and genome coverage) for sequence assembly.
Alejandra Gonzalez-Beltran
PERSON: Jie Zheng, Chris Stoeckert
Philippe Rocca-Serra
NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC
sequence assembly process
true
number of errors
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18.
PMID: 23587118. see table2
a data item that is the number of times that a given process failed, as an integer
Alejandra Gonzalez-Beltran
Philippe Rocca-Serra
PRS, AGB
number of errors
true
true
random access memory size
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18.
PMID: 23587118.
"However, the error correction module in SOAPdenovo was designed for short Illumina reads (35-50 bp), which consumes an excessive amount of computational time and memory on longer reads, for example, over 150 GB memory running for two days using 40-fold 100 bp paired-end Illumina HiSeq 2000 reads"
random access memory size is a scalar measurement datum which denotes the amount of physical memory know as random access memory present of a computer or required by a computational process or data transformation
Alejandra Gonzalez-Beltran
Philippe Rocca-Serra
PRS, AGB
random access memory size
true
random access memory
Random-access memory (RAM) is a form of computer data storage. A random-access device allows stored data to be accessed directly in any random order. In contrast, other data storage media such as hard disks, CDs, DVDs and magnetic tape, as well as early primary memory types such as drum memory, read and write data only in a predetermined order, consecutively, because of mechanical design limitations. Therefore, the time to access a given data location varies significantly depending on its physical location
Alejandra Gonzalez-Beltran
Philippe Rocca-Serra
RAM
http://en.wikipedia.org/wiki/RAM
last accessed: 2013-12-02
random access memory
true
reagent
A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output.
2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device.
PERSON:Matthew Brush
PERSON:Matthew Brush
(copied from ReO)
Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique.
Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated.
In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
reagent
true
secondary cultured cell population
A cultured cell population that is derived through one or more passages in culture.
The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
PERSON:Matthew Brush
secondary cell culture sample
PERSON:Matthew Brush
The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally.
secondary cultured cell population
true
testable hypothesis
that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
An information content entity that expresses an assertion that is intended to be tested.
In the Philly 2013 workshop, we recognized the limitations of "hypothesis textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
Group:2013 Philly Workshop group
hypothesis
Group:2013 Philly Workshop group
testable hypothesis
true
conclusion based on data
The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting.
The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
An information content entity that is inferred from data.
In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
Group:2013 Philly Workshop group
Group:2013 Philly Workshop group
conclusion based on data
true
cell freezing medium
culture media or serum + 10% DMSO is often used as cell freezing media.
A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
PERSON: Matthew Brush
cell freezing medium
true
computation run time
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18.
PMID: 23587118.
See Table 4
computation run time is a time measurement datum which corresponds the time expressed in second, minute, hour necessary for a computer program to complete a process execution, for example genome assembly. It is an important metrics as it indicates the resource occupancy and computer program efficiency.
Alejandra Gonzalez-Beltran
Philippe Rocca-Serra
computation run time datum
PRS,AGB
computation run time
true
mass value specification
A value specification that specifies the mass of some thing.
PERSON:Bjoern Peters
mass value specification
true
categorical value specification
A value specification that is specifies one category out of a fixed number of nominal categories
PERSON:Bjoern Peters
categorical value specification
true
1
1
scalar value specification
A value specification that consists of two parts: a numeral and a unit label
PERSON:Bjoern Peters
scalar value specification
true
value specification
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
PERSON:Bjoern Peters
value specification
true
genome coverage
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18.
PMID: 23587118.
"The genome coverage increased from 81.16% to 93.91%"
A data item that is the total number of bases in reads, divided by genome size, assumed to be the reference size (for instance of 3.10 Gb for human and 2.73 Gb for mouse) and refers to the percentage of the genome that is contained in the assembly based on size estimates; these are usually based on cytological techniques. Genome coverage of 90–95% is generally considered to be good, as most genomes contain a considerable fraction of repetitive regions that are difficult to sequence. So it is not a cause for concern if the genome coverage of an assembly is a bit less than 100%.
Alejandra Gonzalez-Beltran
Philippe Rocca-Serra
A beginner's guide to eukaryotic genome annotation. Yandell M, Ence D.
Nat Rev Genet. 2012 Apr 18;13(5):329-42. doi: 10.1038/nrg3174.
PMID: 22510764
genome coverage
true
N50
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18.
PMID: 23587118.
"Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp"
the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly
Alejandra Gonzalez-Beltran
Philippe Rocca-Serra
weighted median item size
adapted from:
"http://genome.cshlp.org/content/21/12/2224.full?sid=74019122-f944-4ccc-bffe-d16fdd0e7d6c"
(from table 7)
and from "http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html"
N50
true
contig N50
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18.
PMID: 23587118.
"Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp"
N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list.
Alejandra Gonzalez-Beltran
Philippe Rocca-Serra
adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html
contig N50
true
scaffold N50
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18.
PMID: 23587118.
"Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp"
N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information
Alejandra Gonzalez-Beltran
Philippe Rocca-Serra
adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html
scaffold N50
true
RNA Integrity Number value specification
A value specification that specifies the value of the RNA Integrity Number as a real value between 1 (most degraded) and 10 (most intact).
Chris Stoeckert, Bjoern Peters
RIN value specification
OBI
RNA Integrity Number value specification
true
temperature value specification
A value specification that specifies the temperature of some thing.
Chris Stoeckert
OBI
temperature value specification
true
volume value specification
A value specification that specifies the volume of some thing.
Chris Stoeckert
OBI
volume value specification
true
tissue section thickness
A length measurement datum that is the result of an assay measuring the thickness of a tissue section.
Chris Stoeckert, Helena Ellis
NCI BBRB, OBIB
NCI BBRB
tissue section thickness
true
histologic grade according to AJCC 7th edition
G4: Undifferentiated
G1:Well differentiated
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system.
Chris Stoeckert, Helena Ellis
NCI BBRB, OBI
NCI BBRB
histologic grade according to AJCC 7th edition
true
histologic grade according to the Fuhrman Nuclear Grading System
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
Chris Stoeckert, Helena Ellis
Histologic Grade (Fuhrman Nuclear Grading System)
NCI BBRB, OBI
NCI BBRB
histologic grade according to the Fuhrman Nuclear Grading System
true
histologic grade for ovarian tumor
A categorical value specification that is a histologic grade assigned to a ovarian tumor.
Chris Stoeckert, Helena Ellis
NCI BBRB, OBI
NCI BBRB
histologic grade for ovarian tumor
true
histologic grade for ovarian tumor according to a two-tier grading system
A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
Chris Stoeckert, Helena Ellis
NCI BBRB, OBI
NCI BBRB
histologic grade for ovarian tumor according to a two-tier grading system
true
histologic grade for ovarian tumor according to the World Health Organization
A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
Chris Stoeckert, Helena Ellis
NCI BBRB, OBI
NCI BBRB
histologic grade for ovarian tumor according to the World Health Organization
true
pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
Chris Stoeckert, Helena Ellis
pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
true
pathologic primary tumor stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
Chris Stoeckert, Helena Ellis
pT: Pathologic spread lung primary tumor (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic primary tumor stage for lung according to AJCC 7th edition
true
pathologic primary tumor stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
Chris Stoeckert, Helena Ellis
pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic primary tumor stage for kidney according to AJCC 7th edition
true
pathologic primary tumor stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
Chris Stoeckert, Helena Ellis
pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic primary tumor stage for ovary according to AJCC 7th edition
true
pathologic lymph node stage for colon and rectum according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
Chris Stoeckert, Helena Ellis
pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic lymph node stage for colon and rectum according to AJCC 7th edition
true
pathologic lymph node stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
Chris Stoeckert, Helena Ellis
pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic lymph node stage for lung according to AJCC 7th edition
true
pathologic lymph node stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
Chris Stoeckert, Helena Ellis
pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic lymph node stage for kidney according to AJCC 7th edition
true
pathologic lymph node stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
Chris Stoeckert, Helena Ellis
pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic lymph node stage for ovary according to AJCC 7th edition
true
pathologic distant metastases stage for colon according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
Chris Stoeckert, Helena Ellis
M: colon distant metastases (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic distant metastases stage for colon according to AJCC 7th edition
true
pathologic distant metastases stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
Chris Stoeckert, Helena Ellis
M: lung distant metastases (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic distant metastases stage for lung according to AJCC 7th edition
true
pathologic distant metastases stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
Chris Stoeckert, Helena Ellis
M: kidney distant Metastases (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic distant metastases stage for kidney according to AJCC 7th edition
true
pathologic distant metastases stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
Chris Stoeckert, Helena Ellis
M: ovarian distant metastases (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic distant metastases stage for ovary according to AJCC 7th edition
true
clinical tumor stage group according to AJCC 7th edition
A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems.
Chris Stoeckert, Helena Ellis
Clinical tumor stage group (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
clinical tumor stage group according to AJCC 7th edition
true
International Federation of Gynecology and Obstetrics cervical cancer stage value specification
A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems.
Chris Stoeckert, Helena Ellis
Clinical FIGO stage
NCI BBRB, OBI
NCI BBRB
International Federation of Gynecology and Obstetrics cervical cancer stage value specification
true
International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system.
Chris Stoeckert, Helena Ellis
Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)
NCI BBRB, OBI
NCI BBRB
International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
true
performance status value specification
A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life).
Chris Stoeckert, Helena Ellis
Performance Status Scale
https://en.wikipedia.org/wiki/Performance_status
NCI BBRB
performance status value specification
true
Eastern Cooperative Oncology Group score value specification
A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient.
Chris Stoeckert, Helena Ellis
ECOG score
NCI BBRB, OBI
NCI BBRB
Eastern Cooperative Oncology Group score value specification
true
Karnofsky score vaue specification
A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.
Chris Stoeckert, Helena Ellis
Karnofsky Score
NCI BBRB, OBI
NCI BBRB
Karnofsky score vaue specification
true
number of pregnancies
A measurement datum of the total number of pregnancies a woman has had.
Chris Stoeckert, Helena Ellis
NCI BBRB, OBIB
NCI BBRB
number of pregnancies
true
number of live births
A measurement datum of the total number of live births a female has had.
Chris Stoeckert, Helena Ellis
NCI BBRB, OBIB
NCI BBRB
number of live births
true
age when gave birth to first child
An age measurement datum performed on a female when her first biological child was born.
Chris Stoeckert, Helena Ellis
NCI BBRB, OBIB
NCI BBRB
age when gave birth to first child
true
measurand role
A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.
Person: Alan Ruttenberg, Jie Zheng
https://en.wiktionary.org/wiki/measurand
https://github.com/obi-ontology/obi/issues/778
measurand role
true
age since culture seeding measurement datum
An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish).
Stephen A. Fisher, Junhyong Kim, Dan Berrios
age of culture
age since culture seeding measurement datum
true
sequence read length measurement datum
A measurement datum that is the result of the measurement of the number of bases in a DNA or RNA sequence.
Stephen A. Fisher, Junhyong Kim, Dan Berrios
read length, read length measurement datum
sequence read length measurement datum
true
sequencing library input quantity measurement datum
A scalar measurement datum that indicates the amount of sequencing library used as input for a sequencer.
Stephen A. Fisher, Junhyong Kim
library input amount
sequencing library input quantity measurement datum
true
specimen harvest quantity
A scalar measurement datum that indicates the amount of specimen collected.
Stephen A. Fisher, Junhyong Kim, Dan Berrios
harvest quantity
specimen harvest quantity
true
minimum age value specification
A value specifcation that specifies the youngest age when specifying an age range.
Mathias Brochhausen
minimum age value specification
true
maximum age value specification
A value specifcation that specifies the oldest age when specifying an age range.
Mathias Brochhausen
maximum age value specification
true
organism
Drosophila melanogaster
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009:
OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.
This issue is outside the scope of OBI.
GROUP: OBI Biomaterial Branch
James Malone
Jie Zheng
Tomasz Adamusiak
MO_508
NIFSTD:birnlex_376
WEB: http://en.wikipedia.org/wiki/Organism
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. E.g Drosophila melanogaster
organism
organism
EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000634
true
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
PERSON: James Malone
PERSON: Philippe Rocca-Serra
GROUP: OBI Biomaterial Branch
specimen
true
cultured cell population
A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948).
A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
PERSON:Matthew Brush
cell culture sample
PERSON:Matthew Brush
The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.
cultured cell population
true
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A planned process that produces output data from input data.
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Philippe Rocca-Serra
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
data transformation
true
data transformation objective
normalize objective
An objective specification to transformation input data into output data
Modified definition in 2013 Philly OBI workshop
James Malone
PERSON: James Malone
data transformation objective
true
computer
Apple PowerBook, Dell OptiPlex
A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions.
Melanie Courtot
Trish Whetzel
http://en.wikipedia.org/wiki/Computer
computer
true
study design
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
PERSON: Chris Stoeckert
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
study design
true
material component separation
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
a material processing in which components of an input material become segregated in space
Bjoern Peters
IEDB
material component separation
true
maintaining cell culture
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
PlanAndPlannedProcess Branch
OBI branch derived
maintaining cell culture
true
establishing cell culture
a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
PERSON:Matthew Brush
PERSON:Matthew Brush
A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.
establishing cell culture
true
cell culture splitting
The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media.
The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing
PlanAndPlannedProcess Branch
cell culture passaging
OBI branch derived
An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone.
cell culture splitting
true
donor
A T cell line from a PPD(+) donor.
A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro.
IEDB
donor role
IEDB
Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended.
donor
true
A genome is a material entity that represents the entirety of an organism's hereditary information. The genome includes both the genes and the non-coding sequences of the DNA and RNA.
Oliver He
Book: Eugene Nester, Denise Anderson, C. Evans Roberts, Jr., Microbiology (Companion Site): A Human Perspective, 7th Edition. Mcgraw Hill, October 18, 2011. ISBN-13: 978-0073375311
WEB: http://en.wikipedia.org/wiki/Genome
genome
true
A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule.
Oliver He
WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/
In addition to the coding regions (exons), a gene includes transcription-control regions and sometimes introns. Although the majority of genes encode proteins, some encode tRNAs, rRNAs, and other types of RNA.
gene
true
a disposition that a gene can be used as a blueprint for generating a new form of product such as protein.
Yongqun He
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
YH: According to NCBI Gene project, there are two gene types: unknown (0) , tRNA (1) , rRNA (2) , snRNA (3) , scRNA (4) , snoRNA (5) , protein-coding (6) , pseudo (7) , transposon (8) , miscRNA (9) , ncRNA (10) , other (255). Therefore, we have generated corresponding gene dispositions. Note that we don't use the term "gene type" here to differentiate the meanings of "type" and "disposition".
gene disposition
true
a gene disposition that a gene can be used as a blueprint for generating a protein (i.e., a gene encodes for a protein).
Yongqun He
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
protein-coding gene disposition
true
a gene disposition that represents the disposition of gene being "pseudo", i.e., the gene is a pseudogene.
Yongqun He
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
pseudo gene disposition
true
The genome of an organism of Eukaryota
Yue Liu, Bin Zhao, Oliver He
2759
genome of Eukaryota
true
The genome of an organism of Homo sapiens
Yue Liu, Bin Zhao, Oliver He
9606
genome of Homo sapiens
true
A gene of an organism of Eukaryota
Yue Liu, Bin Zhao, Oliver He
2759
gene of Eukaryota
true
A gene of an organism of Homo sapiens
Yue Liu, Bin Zhao, Oliver He
9606
gene of Homo sapiens
true
A gene of Homo sapiens that has a protein-coding gene disposition
Bin Zhao, Oliver He
9606
protein-coding gene of Homo sapiens
true
A gene of Homo sapiens that has a pseudo gene disposition
Bin Zhao, Oliver He
9606
pseudo gene of Homo sapiens
true
Bin Zhao, Yue Liu, Oliver He
AAT6
ACTSA
MYMY5
WEB: http://www.ncbi.nlm.nih.gov/gene
https://www.ncbi.nlm.nih.gov/pubmed/28117838
ACTA2
actin, alpha 2, smooth muscle, aorta
59
GIG46
10q23.3
20140408
9606
10
protein-coding
Official from a nomenclature committee
GO_0005524 (EC: IEA); GO_0005615 (EC: IDA); GO_0005737 (EC: IDA, PMID: 12355421); GO_0005829 (EC: TAS); GO_0006936 (EC: TAS); GO_0008217 (EC: IEA); GO_0009615 (EC: IEP, PMID: 16548883); GO_0014829 (EC: IEA); GO_0015629 (EC: IEA); GO_0030485 (EC: IEA); GO_0043234 (EC: IDA, PMID: 18468998); GO_0072144 (EC: IEP, PMID: 17464107)
PMID: 1540415; 1555776; 1907279; 1939373; 1969628; 1991513; 2022339; 2295650; 2398629; 2612915; 2701935; 3842206; 6330528; 6725286; 7780165; 8138584; 8997639; 9512352; 9546431; 9841925; 10341211; 10556093; 10628374; 11037796; 11580270; 11707283; 11812134; 12119014; 12355421; 12477932; 12777385; 14530271; 14627618; 14694110; 15032605; 15164054; 15342556; 15489334; 15555551; 15588509; 15618548; 15703204; 15862967; 16051665; 16115228; 16289162; 16385451; 16526095; 16548883; 16573163; 17360745; 17411366; 17464107; 17504171; 17626241; 17786474; 17994018; 18443296; 18468998; 18775311; 18781797; 19261809; 19285011; 19409525; 19531499; 19639585; 19639654; 19654303; 19683985; 19745835; 19788615; 19883584; 19913121; 20128380; 20132408; 20147394; 20237496; 20301299; 20381122; 20618440; 20628086; 20628268; 20639865; 20689142; 20694011; 20734336; 20876399; 20970362; 20972266; 21131735; 21139048; 21145461; 21212136; 21233699; 21248741; 21288906; 21343850; 21477997; 21496259; 21530503; 21553326; 21612641; 21617610; 21815248; 21890473; 21906983; 21917091; 21923909; 21937134; 21937873; 21963094; 21987572; 21996542; 22001912; 22004035; 22053931; 22133903; 22138123; 22232431; 22395512; 22460095; 22465675; 22479424; 22505724; 22535526; 22543453; 22619371; 22790431; 22810585; 22831780; 22939629; 22946110; 22960022; 22989508; 23000965; 23020218; 23068445; 23116162; 23182716; 23246001; 23770605; 23788249; 23794425; 23982059; 24244333
actin, alpha 2, smooth muscle, aorta
Ensembl:ENSG00000107796
HGNC:130
HPRD:00031
MIM:102620
Vega:OTTHUMG00000018700
Other designations: actin, aortic smooth muscle|alpha-cardiac actin|cell growth-inhibiting gene 46 protein
This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838
ACTA2
true
Bin Zhao, Yue Liu, Oliver He
ANK
SPH1
SPH2
WEB: http://www.ncbi.nlm.nih.gov/gene
ANK1
ankyrin 1, erythrocytic
286
8p11.1
20140408
9606
8
protein-coding
Official from a nomenclature committee
GO_0005198 (EC: NAS, PMID: 9430667); GO_0005200 (EC: TAS, PMID: 8640229); GO_0005515 (EC: IPI, PMID: 12527750); GO_0005634 (EC: IEA); GO_0005829 (EC: TAS); GO_0005856 (EC: NAS, PMID: 1833445); GO_0005886 (EC: IDA, PMID: 379653); GO_0005886 (EC: NAS, PMID: 9430667); GO_0006779 (EC: IEA); GO_0006887 (EC: NAS, PMID: 1833445); GO_0006888 (EC: IDA, PMID: 18768923); GO_0007010 (EC: NAS, PMID: 9430667); GO_0007165 (EC: IEA); GO_0007411 (EC: TAS); GO_0008093 (EC: IDA, PMID: 379653); GO_0008093 (EC: TAS, PMID: 11427698); GO_0010638 (EC: IEA); GO_0014731 (EC: IDA, PMID: 379653); GO_0015672 (EC: IEA); GO_0016323 (EC: NAS, PMID: 12409278); GO_0016529 (EC: IEA); GO_0019899 (EC: IPI); GO_0019899 (EC: TAS, PMID: 11427698); GO_0030018 (EC: IEA); GO_0030507 (EC: IDA, PMID: 379653); GO_0030507 (EC: IPI, PMID: 8159688); GO_0030507 (EC: NAS, PMID: 8640229); GO_0030673 (EC: IEA); GO_0030863 (EC: IEA); GO_0031430 (EC: IEA); GO_0042383 (EC: IEA); GO_0045199 (EC: TAS, PMID: 11427698); GO_0045211 (EC: IEA); GO_0048821 (EC: IEA); GO_0051117 (EC: IPI, PMID: 8159688); GO_0072661 (EC: IMP, PMID: 18768923)
PMID: 379653; 492324; 1689849; 1833445; 2137557; 2141335; 2968981; 2970468; 2971657; 6449514; 7505012; 8125298; 8159688; 8227202; 8385102; 8640229; 8681137; 8703812; 9024692; 9235914; 9430667; 9519902; 9587054; 9628825; 9804856; 10893266; 10910934; 11222639; 11372755; 11427698; 12019270; 12130521; 12409278; 12444090; 12456646; 12477932; 12527750; 12543979; 12631729; 12719424; 15040428; 15051494; 15489334; 15929114; 16580865; 16597699; 16718373; 16762928; 16962094; 17128827; 17207965; 17520478; 17716929; 17720975; 18768923; 18987618; 20379614; 20479128; 20858683; 21071415; 21099109; 21177872; 21493712; 22348230; 22424883; 22456796; 22573887; 22968456; 23013433; 23457408
ankyrin 1, erythrocytic
Ensembl:ENSG00000029534
HGNC:492
HPRD:01693
MIM:612641
Vega:OTTHUMG00000150281
Other designations: ANK-1|ankyrin-1|ankyrin-R|erythrocyte ankyrin
This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838
ANK1
true
Bin Zhao, Yue Liu, Oliver He
SM22
SMCC
TAGLN1
WS3-10
WEB: http://www.ncbi.nlm.nih.gov/gene
TAGLN
transgelin
6876
11q23.2
20140408
9606
11
protein-coding
Official from a nomenclature committee
GO_0003779 (EC: IEA); GO_0005515 (EC: IPI); GO_0005737 (EC: IEA); GO_0007517 (EC: TAS, PMID: 9615232); GO_0030855 (EC: IDA)
PMID: 1520290; 1872880; 7788527; 8117285; 8125298; 9242426; 9276683; 9384215; 9615232; 11053353; 11773051; 12200029; 12477932; 12521938; 15489334; 16009940; 17082327; 17305610; 17353931; 17629319; 18245174; 18291675; 18378184; 18446369; 19011151; 19188659; 19329940; 19724680; 19796641; 19848416; 19913121; 20012321; 20066125; 20098441; 20336793; 20379614; 20540360; 20628086; 20705054; 20707403; 21044950; 21051832; 21092460; 21139048; 21677441; 21763649; 21943158; 22245152; 22257561; 22365974; 22939629; 23138394; 23174934; 23331552; 23538046; 23824909
transgelin
Ensembl:ENSG00000149591
HGNC:11553
HPRD:02891
MIM:600818
Vega:OTTHUMG00000167067
Other designations: 22 kDa actin-binding protein|SM22-alpha|smooth muscle protein 22-alpha|transgelin variant 2
This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838
TAGLN
true
Bin Zhao, Yue Liu, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
VGF
VGF nerve growth factor inducible
7425
7q22.1
20140408
9606
7
protein-coding
Official from a nomenclature committee
GO_0001541 (EC: IEA); GO_0002021 (EC: IEA); GO_0003674 (EC: ND); GO_0005184 (EC: IEA); GO_0005615 (EC: IDA, PMID: 15706611); GO_0006091 (EC: IEA); GO_0008083 (EC: IEA); GO_0009409 (EC: IEA); GO_0019953 (EC: IEA); GO_0030073 (EC: IEA); GO_0030133 (EC: IEA); GO_0031410 (EC: IDA, PMID: 17440014); GO_0032868 (EC: IEA); GO_0042593 (EC: IEA); GO_0042742 (EC: IEA); GO_0051591 (EC: IEP, PMID: 10381005)
PMID: 8125298; 9084409; 9344675; 10381005; 12477932; 15706611; 16481598; 17440014; 17684500; 18432310; 19598235; 20164831; 20471433; 20631166; 21151573; 21621608; 22808091; 24244333; 24250222; 24457600
VGF nerve growth factor inducible
Other designations: neuro-endocrine specific protein VGF|neurosecretory protein VGF
This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838
VGF
true
Bin Zhao, Yue Liu, Oliver He
MST092
MST106
MST129
MSTP032
MSTP092
MSTP106
MSTP129
WEB: http://www.ncbi.nlm.nih.gov/gene
RGS5
regulator of G-protein signaling 5
8490
RP11-267N12.3
1q23.1
20140408
9606
1
protein-coding
Official from a nomenclature committee
GO_0005096 (EC: IBA); GO_0005737 (EC: IDA); GO_0005886 (EC: IBA); GO_0007165 (EC: IEA); GO_0008277 (EC: TAS, PMID: 10471929); GO_0038032 (EC: IEA); GO_0043547 (EC: IBA); GO_0043547 (EC: TAS, PMID: 10471929)
PMID: 9079700; 9747037; 10471929; 11009569; 11076863; 11230166; 11253162; 12477932; 14755443; 15342556; 15459006; 15489334; 15489336; 15670159; 16293795; 16344560; 16381901; 16710414; 17100651; 17220356; 17762159; 17939118; 18029348; 18262772; 18676680; 19170196; 19488044; 19536175; 19564336; 19625176; 19692168; 19863299; 20379614; 20453000; 20627871; 20643937; 21105200; 21278382; 21393447; 21780128; 21832049; 21881522; 22130514; 23464602; 23868206; 24009623; 24124411; 24297163
regulator of G-protein signaling 5
Ensembl:ENSG00000143248
Ensembl:ENSG00000232995
HGNC:10001
HPRD:04471
MIM:603276
Vega:OTTHUMG00000034441
This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838
RGS5
true
Bin Zhao, Yue Liu, Oliver He
GABABR2
GPR51
GPRC3B
HG20
HRIHFB2099
WEB: http://www.ncbi.nlm.nih.gov/gene
GABBR2
gamma-aminobutyric acid (GABA) B receptor, 2
9568
9q22.1-q22.3
20140408
9606
9
protein-coding
Official from a nomenclature committee
GO_0004965 (EC: IDA, Qualifier: contributes_to, PMID: 9872316); GO_0005515 (EC: IPI, PMID: 16724110); GO_0005737 (EC: IEA); GO_0005886 (EC: TAS); GO_0005887 (EC: IDA, PMID: 9872316); GO_0007186 (EC: TAS, PMID: 9872316); GO_0007194 (EC: TAS, PMID: 10328880); GO_0007214 (EC: IDA, PMID: 9872316); GO_0007268 (EC: TAS); GO_0030054 (EC: IEA); GO_0038039 (EC: IPI, PMID: 9872316); GO_0043005 (EC: IEA); GO_0045211 (EC: IEA)
PMID: 2834384; 7494864; 9872316; 9872317; 10075644; 10087195; 10328880; 10727622; 10773016; 11087824; 11850456; 11854302; 12477932; 14625043; 14961561; 14966130; 14978362; 15164053; 15489334; 15660124; 15822905; 16169070; 16724110; 16829628; 17145756; 17185339; 18482426; 18577758; 18978678; 19002745; 19086053; 19308021; 19336370; 19744961; 19763258; 20379614; 20424473; 20467438; 20557420; 20583170; 20634891; 20734064; 21303731; 21724853; 21971078; 22169202; 22613715; 22660477; 23726511; 23864651
gamma-aminobutyric acid (GABA) B receptor, 2
Ensembl:ENSG00000136928
HGNC:4507
HPRD:09552
MIM:607340
Vega:OTTHUMG00000020345
Other designations: G protein-coupled receptor 51|G-protein coupled receptor 51|GABA-B receptor 2|GABA-B receptor, R2 subunit|GABA-B-R2|GABA-BR2|gamma-aminobutyric acid B receptor 2|gamma-aminobutyric acid type B receptor subunit 2|gb2
This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838
GABBR2
true
Bin Zhao, Yue Liu, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
COL5A3
collagen, type V, alpha 3
50509
19p13.2
20140408
9606
19
protein-coding
Official from a nomenclature committee
GO_0005201 (EC: NAS, PMID: 10722718); GO_0005518 (EC: NAS, PMID: 10722718); GO_0005576 (EC: TAS); GO_0005588 (EC: NAS, PMID: 10722718); GO_0005788 (EC: TAS); GO_0007160 (EC: IEA); GO_0007411 (EC: TAS); GO_0008201 (EC: IEA); GO_0022617 (EC: TAS); GO_0030198 (EC: TAS); GO_0030199 (EC: NAS, PMID: 10722718); GO_0030574 (EC: TAS); GO_0043394 (EC: IEA); GO_0043588 (EC: NAS, PMID: 10722718)
PMID: 1571108; 1916105; 6501291; 7115902; 7346227; 8535602; 9443080; 10722718; 11423559; 15136578; 15316020; 19012342
collagen, type V, alpha 3
Other designations: collagen alpha-3(V) chain|pro-(alpha)3(V) collagen
This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838
COL5A3
true
Bin Zhao, Yue Liu, Oliver He
CLR19.9
NALP2
NBS1
PAN1
PYPAF2
WEB: http://www.ncbi.nlm.nih.gov/gene
https://www.ncbi.nlm.nih.gov/pubmed/28117838
NLRP2
NLR family, pyrin domain containing 2
55655
XXbac-BPG230H20.8
19q13.42
20140408
9606
19
protein-coding
Official from a nomenclature committee
GO_0005515 (EC: IPI, PMID: 15030775); GO_0005524 (EC: IEA); GO_0005737 (EC: IDA, PMID: 15030775); GO_0032090 (EC: IPI, PMID: 15030775); GO_0043280 (EC: IDA, PMID: 15030775); GO_0050718 (EC: IDA, PMID: 15030775)
PMID: 8125298; 11250163; 11270363; 12019269; 12387869; 12477932; 12563287; 14702039; 15030775; 15456791; 15489334; 15817483; 16344560; 17046979; 17178784; 17420470; 17435760; 18056399; 18285453; 18369178; 18772453; 19074885; 19103770; 19300480; 19534089; 19900269; 20403135; 20800603; 21832049; 21906983; 21976665; 22909446; 23128233; 23360675; 23625868; 23644288
NLR family, pyrin domain containing 2
Ensembl:ENSG00000022556
HGNC:22948
HPRD:14805
MIM:609364
Vega:OTTHUMG00000167763
Other designations: NACHT, LRR and PYD containing protein 2|NACHT, LRR and PYD domains-containing protein 2|NACHT, leucine rich repeat and PYD containing 2|PYRIN domain and NACHT domain-containing protein 1|PYRIN-containing APAF1-like protein 2|nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2|nucleotide-binding site protein 1
This gene is upregulated at neural stem cell stage and at iPSC stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838
NLRP2
true
Bin Zhao, Yue Liu, Oliver He
CBP
PAG
WEB: http://www.ncbi.nlm.nih.gov/gene
PAG1
phosphoprotein associated with glycosphingolipid microdomains 1
55824
8q21.13
20140408
9606
8
protein-coding
Official from a nomenclature committee
GO_0005070 (EC: NAS, PMID: 10790433); GO_0005515 (EC: IPI, PMID: 10790433); GO_0005886 (EC: IDA, PMID: 10790433); GO_0005886 (EC: TAS); GO_0007165 (EC: TAS, PMID: 10790433); GO_0007173 (EC: TAS); GO_0009967 (EC: NAS, PMID: 10790433); GO_0016021 (EC: IEA); GO_0035556 (EC: IDA, PMID: 10790433); GO_0042169 (EC: IDA, PMID: 10790433); GO_0045121 (EC: IDA, PMID: 10790433); GO_0050852 (EC: TAS); GO_0050863 (EC: IDA, PMID: 10790433); GO_0050868 (EC: IEA)
PMID: 9334312; 10790433; 11163757; 11684085; 12477932; 12665526; 14665621; 14702039; 15489334; 16160011; 16413409; 16636672; 16947079; 17143285; 17389760; 18056706; 18070987; 19581936; 19913121; 20379614; 20388373; 20561033; 20628086; 21092590; 21156787; 21388951; 21822266; 22027792; 22659621; 22994656; 23022100; 23671581
phosphoprotein associated with glycosphingolipid microdomains 1
Ensembl:ENSG00000076641
HGNC:30043
HPRD:05772
HPRD:16944
MIM:605767
Vega:OTTHUMG00000164592
Other designations: Csk-binding protein|phosphoprotein associated with glycosphingolipid-enriched microdomains 1|transmembrane adapter protein PAG|transmembrane adaptor protein PAG|transmembrane phosphoprotein Cbp
This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838
PAG1
true
Bin Zhao, Yue Liu, Oliver He
CPI17-like
KEPI
NY-BR-81
WEB: http://www.ncbi.nlm.nih.gov/gene
PPP1R14C
protein phosphatase 1, regulatory (inhibitor) subunit 14C
81706
6q24.3-q25.3
20140408
9606
6
protein-coding
Official from a nomenclature committee
GO_0004865 (EC: IEA); GO_0005737 (EC: IEA); GO_0016020 (EC: IEA); GO_0042325 (EC: IEA)
PMID: 11564868; 11812771; 11948623; 12477932; 12747765; 14574404; 14702039; 15489334; 16449650; 19132087; 19475667; 20592344; 21946350; 22939629; 23284291
protein phosphatase 1, regulatory (inhibitor) subunit 14C
Ensembl:ENSG00000198729
HGNC:14952
HPRD:17890
MIM:613242
Vega:OTTHUMG00000015818
Other designations: PKC-potentiated PP1 inhibitory protein|kinase C-enhanced PP1 inhibitor|kinase-enhanced PP1 inhibitor|protein phosphatase 1 regulatory subunit 14C|serologically defined breast cancer antigen NY-BR-81
This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838
PPP1R14C
true
Bin Zhao, Yue Liu, Oliver He
CEACAM3
R29124_1
WEB: http://www.ncbi.nlm.nih.gov/gene
CEACAM21
carcinoembryonic antigen-related cell adhesion molecule 21
90273
UNQ3098/PRO10075
19q13.2
20140408
9606
19
protein-coding
Official from a nomenclature committee
GO_0016021 (EC: IEA)
PMID: 12477932; 12975309; 14702039; 21682944; 23065704
carcinoembryonic antigen-related cell adhesion molecule 21
Ensembl:ENSG00000007129
HGNC:28834
HPRD:10179
Vega:OTTHUMG00000151062
This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838
CEACAM21
true
Bin Zhao, Yue Liu, Oliver He
UNQ26
bet
WEB: http://www.ncbi.nlm.nih.gov/gene
DNER
delta/notch-like EGF repeat containing
92737
UNQ262/PRO299
2q36.3
20140408
9606
2
protein-coding
Official from a nomenclature committee
GO_0001764 (EC: NAS, PMID: 11950833); GO_0004888 (EC: TAS, PMID: 11950833); GO_0005112 (EC: IEA); GO_0005509 (EC: NAS, PMID: 11950833); GO_0005515 (EC: IPI, PMID: 11950833); GO_0005769 (EC: IDA, PMID: 11950833); GO_0005886 (EC: IDA, PMID: 11950833); GO_0006897 (EC: NAS, PMID: 11950833); GO_0007219 (EC: TAS); GO_0007220 (EC: IEA); GO_0007416 (EC: NAS, PMID: 11950833); GO_0007417 (EC: IEP, PMID: 11950833); GO_0010001 (EC: IEA); GO_0016021 (EC: IEA); GO_0030276 (EC: TAS, PMID: 11950833); GO_0030425 (EC: IDA, PMID: 11950833); GO_0043025 (EC: IEA); GO_0048741 (EC: IEA)
PMID: 9847074; 11950833; 11997712; 12477932; 12975309; 15489334; 15815621; 16344560; 16740002; 20070733; 20237496; 20367751; 23284291; 23382691; 24101674
delta/notch-like EGF repeat containing
Ensembl:ENSG00000187957
HGNC:24456
HPRD:09531
MIM:607299
Vega:OTTHUMG00000153637
Other designations: H_NH0150O02.1|WUGSC:H_NH0150O02.1|delta and Notch-like epidermal growth factor-related receptor|delta-notch-like EGF repeat-containing transmembrane
This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838
DNER
true
Bin Zhao, Yue Liu, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
EEF1A1P16
eukaryotic translation elongation factor 1 alpha 1 pseudogene 16
387845
12p12.3
20140408
9606
12
pseudo
Official from a nomenclature committee
eukaryotic translation elongation factor 1 alpha 1 pseudogene 16
This gene is upregulated at iPSC stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838
EEF1A1P16
true
An ethnic identity datum that is the output of an ethnic identification process that uses OMB terminology for ethnicity or terminology that is mapped the OMB ethnicity terms.
Amanda Hicks
OMB ethnic identity datum
true
A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
racial identity datum
true
racial identification process
true
An ethnic identity datum is an information content entity that is the output of some ethnic identitification process and is intended to be a truthful statement about the cultural or national heritage of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
Amanda Hicks
ethnic identity datum
true
ethnic identification process
true
An OMB ethnic identity datum that indicates the person identified is of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race.
Amanda Hicks
hispanic or latino identity datum
true
An OMB ethnic identity datum that indicates the person identified is not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race.
Amanda Hicks
not hispanic or latino identity datum
true
An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method.
Amanda Hicks
identity datum
true
A gender identity is an information content entity that is the output of some gender identitification process and is intended to be a truthful statement about a person's subjective sense of their gender. Unlike data items they are not necessilary contributed or acquired by a reliable method.
Amanda Hicks
gender identity datum
true
Amanda Hicks
identification process
true
true
gender identification process
true
a gender identity datum resulting from a gender identification process in which ‘female’ is selected based on the participant's subjective sense of gender
Amanda Hicks
female gender identity datum
true
a gender identity datum resulting from a gender identification process in which ‘male’ is selected based on the participant's subjective sense of gender
Amanda Hicks
male gender identity datum
true
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment.
Amanda Hicks
American Indian or Alaska Native identity datum
true
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent.
Amanda Hicks
Asian identity datum
true
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the black racial groups of Africa.
Amanda Hicks
black or African American identity datum
true
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands.
Amanda Hicks
Native Hawaiian or other Pacific Islander identity datum
true
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Europe, the Middle East, or North Africa.
Amanda Hicks
white identity datum
true
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms.
Amanda Hicks
OMB racial identity datum
true
A measurement datum that records how many times a cell culture has been subcultured.
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T21:47:04Z
cell cutlture passage number
true
gene marker role
true
stem cell marker process
true
neural stem cell marker process
true
iPSC marker process
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T22:04:02Z
stem cell producer
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T22:05:33Z
stem cell provider
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T22:44:27Z
age of donor at time of donation
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T22:49:56Z
cell line testing laboratory
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T23:01:40Z
feeder cell role
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T23:03:57Z
feeder cell
true
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T23:05:48Z
feeder cell preparation protocol
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T23:08:01Z
source cell storage/master cell banking protocol
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T23:09:23Z
source cell procurement protocol
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T23:10:11Z
material transferring protocol
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T23:10:35Z
cell passage protocol
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T23:11:25Z
establishment protocol (molecular induction protocol)
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-05-31T23:12:12Z
cell culture protocol
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-06-05T17:59:34Z
donor
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-06-05T19:08:22Z
TeSR
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-06-05T19:08:39Z
DMEM
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-06-05T19:08:58Z
F12
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-06-05T19:15:48Z
cell culture additive role
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-06-05T19:18:35Z
cell culture medium additive
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-06-05T19:24:37Z
concentration measurment datum
true
age
A time quality inhering in a bearer by virtue of how long the bearer has existed.
age
true
biological sex
James Malone
Jie Zheng
Tomasz Adamusiak
biological sex
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#sex
MO_680
NCIt:C28421
PATO:0000047
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny.
The assemblage of physical properties or qualities by which male is distinguished from female; the physical difference between male and female; the distinguishing peculiarity of male or female.
biological sex
sex
EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000695
true
length
A 1-D extent quality which is equal to the distance between two points.
length
true
mass
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
mass
true
temperature
A physical quality of the thermal energy of a system.
temperature
true
behavioral quality
An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation.
behavioral quality
true
James Malone
Jie Zheng
Tomasz Adamusiak
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#male
CARO:0000027
MO_652
PATO:0000384
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
male
true
volume
A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
volume
true
quality of a single physical entity
A physical object quality which inheres in a single-bearer.
quality of a single physical entity
true
physical object quality
physical object quality
true
cellular quality
true
cellular potency
cellular potency
true
unipotent
true
multipotent
multipotent
true
pluripotent
pluripotent
true
organismal quality
organismal quality
true
handedness
A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet.
handedness
true
left handedness
Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
left handedness
true
right handedness
Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
right handedness
true
ambidextrous handedness
Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot.
ambidextrous handedness
true
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
protein
true
A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction.
B-lymphocyte surface antigen B4
CD19
T-cell surface antigen Leu-12
differentiation antigen CD19
CD19 molecule
true
A protein that is a translation product of the human CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved.
CD34
hematopoietic progenitor cell antigen CD34
CD34 molecule
true
A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence.
CD4
T-cell differentiation antigen L3T4
T-cell surface antigen T4/Leu-3
T-cell surface glycoprotein CD4
CD4 molecule
true
An integrin alpha that contains an A domain. A hallmark of this class is the presence of a von Willebrand factor type A domain (Pfam:PF00092) (I-domain) of approximately 200 amino acid residues at the N terminus, which confers divalent cation binding properties. Unlike other integrin alpha proteins, they do not undergo proteolytic cleavage.
integrin alpha with I domain
integrin alpha with A domain
true
A protein that is a translation product of the human PTPRC gene or a 1:1 ortholog thereof. It is composed of an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic protein-tyrosine phosphatase domains. Contains 1 to 3 copies of the Fibronectin type III domain (Pfam:PF00041) followed by two copies of the Protein-tyrosine phosphatase (Pfam:PF00102) domain. Receptor-type tyrosine-protein phosphatase C (CD45) regulates signal transduction and lymphocyte activation by specific association with receptor molecules on T and B cells. Multiple isoforms of CD45 (180-235 kDa) can be generated asa result of alternative splicing of three variable exons 4(A), 5(B) and 6(C), encoding sequences at the N-terminal extracellular domain of the molecule.
T200
CD45
L-CA
PTPRC
leukocyte common antigen
ly-5
lymphocyte antigen 5
receptor-type tyrosine-protein phosphatase C
true
An integrin alpha with A domain that is a translation product of the human ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1.
CD11 antigen-like family member B
CD11b
CR-3 alpha chain
ITGAM
cell surface glycoprotein MAC-1 subunit alpha
leukocyte adhesion receptor MO1
neutrophil adherence receptor
CR3A
integrin alpha-M
true
A receptor-type tyrosine-protein phosphatase C that is a translation product of a mature transcript of the PTPRC gene, that includes the region encoded by the variable exons 4(A), 5(B), and 6(C). Example: UniProtKB:P08575-1.
CD45R
CD45RABC
PTPRC/iso:CD45R
B220
receptor-type tyrosine-protein phosphatase C isoform CD45R
true
A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response.
CD3 subunit with Ig-like domain
CD3 subunit with immunoglobulin domain
true
A CD3 subunit with immunoglobulin domain that is a translation product of the human CD3E gene or a 1:1 ortholog thereof.
CD3E
CD3e
T-cell surface antigen T3/Leu-4 epsilon chain
T3E
CD3 epsilon
true
A protein with a domain composition consisting of a large extracellular domain, including five Ig-like C2-type domains followed by two copies of the Fibronectin type-III domain (Pfam:PF00041), a single-pass transmembrane domain and a short cytoplasmic C-terminal domain.
neural cell adhesion molecule
true
A neural cell adhesion molecule that is involved in neuronal development, synaptic plasticity, and regeneration.
neural cell adhesion molecule NCAM
true
A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof.
CD56
N-CAM-1
NCAM-1
NCAM1
NCAM
neural cell adhesion molecule 1
true
A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof.
CD2
LFA-2
LFA-3 receptor
T-cell surface antigen CD2
T-cell surface antigen T11/Leu-5
T-cell surface glycoprotein CD2
erythrocyte receptor
ly-37
lymphocyte antigen 37
rosette receptor
SRBC
CD2 molecule
true
A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain.
CD8A
CD8a
T-cell surface glycoprotein Lyt-2
T-lymphocyte differentiation antigen T8/Leu-2
Lyt-2
Lyt2
MAL
T-cell surface glycoprotein CD8 alpha chain
true
A protein that contains the ADP-ribosyl cyclase domain (Pfam:PF02267).
ADP-ribosyl cyclase
true
A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof.
B-cell differentiation antigen Ly-44
B-cell surface antigen CD20
B-lymphocyte antigen CD20
B-lymphocyte surface antigen B1
Bp35
CD20
MS4A1
leukocyte surface antigen Leu-16
lymphocyte antigen 44
Ly-44
Ms4a2
membrane-spanning 4-domains subfamily A member 1
true
A protein that is a translation product of the human CD44 gene or a 1:1 ortholog thereof.
CD44
CD44 antigen
CDw44
ECMR-III
GP90 lymphocyte homing/adhesion receptor
HUTCH-I
PGP-1
epican
extracellular matrix receptor III
heparan sulfate proteoglycan
hermes antigen
hyaluronate receptor
ly-24
lymphocyte antigen 24
phagocytic glycoprotein 1
phagocytic glycoprotein I
LHR
MDU2
MDU3
MIC4
PGP-I
CD44 molecule
true
A protein that is a translation product of the human CD48 gene or a 1:1 ortholog thereof.
B-lymphocyte activation marker BLAST-1
BCM1 surface antigen
BLAST-1
CD48
CD48 antigen
HM48-1
MRC OX-45 surface antigen
TCT.1
leukocyte antigen MEM-102
sgp-60
BCM1
BLAST1
Bcm-1
CD48 molecule
true
A protein that has a core domain structure of signal sequence, propeptide, five Cadherin domains (Pfam:PF00028), a transmembrane region, and a Cadherin cytoplasmic region (Pfam:PF01049). Cadherins function as adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in solid tissues.
cadherin
true
A protein that is a translation product of the human ENG gene or a 1:1 ortholog thereof.
CD105
ENG
cell surface MJ7/18 antigen
END
Edg
endoglin
true
A protein with a core domain architecture consisting of an extracellular domain containing two copies of the Immunoglobulin domain (Pfam:PF00047), followed by a single-pass transmembrane region and a small intracellular domain. The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. Human II-a, II-b, and II-c represent a recent gene expansion and are equally related to mouse II, III, and IV. Human III-A and III-B are closely related and closer to mouse IV than to mouse III.
immunoglobulin gamma Fc receptor II/III/IV
true
An ADP-ribosyl cyclase that is a translation product of the human CD38 gene or a 1:1 ortholog thereof.
CD38
I-19
NIM-R5 antigen
T10
cADPr hydrolase 1
cyclic ADP-ribose hydrolase 1
ADP-ribosyl cyclase 1
true
A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof.
7B4 antigen
CD144
CDH5
VE-cadherin
vascular endothelial cadherin
cadherin-5
true
An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr3 gene or a 1:1 ortholog thereof.
CD16
Fc-gamma RIII
FcRIII
Fcgr3
IgG Fc receptor III
low affinity immunoglobulin gamma Fc region receptor III
true
A protein with core architecture consisting of one Prominin (Pfam:PF05478) domain. The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and human prominin and prominin-like 1 are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain.
prominin
true
A prominin that is a translation product of the human PROM1 gene or a 1:1 ortholog thereof.
CD133
PROM1
antigen AC133
antigen AC133 homolog
prominin-like protein 1
PROML1
Prom
prominin-1
true
A protein that is a translation product of the human NT5E gene or a 1:1 ortholog thereof.
5'-NT
CD73
NT5E
ecto-5'-nucleotidase
NT5
NTE
5'-nucleotidase
true
A protein that is a translation product of the CD59 or closely related gene. This gene is present as a single copy in human and has undergone a lineage-specific duplication in mouse. CD59 antigen has a core architecture consisting of one UPAR/Ly-6 domain (Pfam:PF00021), a small domain of about 70 amino acids and containing 5 conserved disulfide bonds. It is both N- and O-glycosylated and is a GPI-anchored protein that releases soluble forms in some tissues.
CD59-like glycoprotein
true
A protein with core architecture consisting of asignal sequence, 5 Ig-like domains, followed by a transmembrane sequence, followed by a Protein tyrosine kinase domain (Pfam:PF07714). However, only 1-3 of the Ig domains are detected by the Pfam HMMs in most of the sequences. Pfam:PF00047 is most common, but other members of the Ig domain clan, Pfam:PF07679 and Pfam:PF07686 can be identified instead. The fourth Ig domain lacks the disulfide-bonded cysteines.
CSF-1/PDGF receptor-type tyrosine-protein kinase
true
A protein that is a translation product of the human SLAMF1 gene or a 1:1 ortholog thereof.
CD150
CDw150
IPO-3
SLAMF1
SLAM
SLAM family member 1
true
A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof.
CD5
Lyt-1
ly-1
lymphocyte antigen 1
lymphocyte antigen T1/Leu-1
LEU1
T-cell surface glycoprotein CD5
true
A protein that is a translation product of the human THY1 gene or a 1:1 ortholog thereof.
CD90
CDw90
THY1
Thy-1 antigen
Thy-1
Thy-1 membrane glycoprotein
true
A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof.
CD127
CDw127
IL-7 receptor subunit alpha
IL-7R subunit alpha
IL-7R-alpha
IL-7RA
IL7R
interleukin-7 receptor subunit alpha
true
A protein that is a translation product of the KLRB1 gene or its closely related paralogs (KLRB1A-F). There are lineage-specific expansions in mouse and rat.
KLRB1-like protein
true
A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof.
CD14
monocyte differentiation antigen CD14
myeloid cell-specific leucine-rich glycoprotein
CD14 molecule
true
A protein that is a translation product of the human CD33 gene or a 1:1 ortholog thereof.
CD33
gp67
myeloid cell surface antigen CD33
sialic acid-binding Ig-like lectin 3
siglec-3
SIGLEC3
CD33 molecule
true
A protein that is a translation product of the human CD244 gene or a 1:1 ortholog thereof.
CD244
NAIL
NK cell activation-inducing ligand
NK cell type I receptor protein 2B4
NKR2B4
non-MHC restricted killing associated
2B4
Nmrk
natural killer cell receptor 2B4
true
A protein that is a translation product of the human CD24 gene or a 1:1 ortholog thereof.
CD24
HSA
M1/69-J11D heat stable antigen
R13-Ag
X62 heat stable antigen
ly-52
lymphocyte antigen 52
nectadrin
small cell lung carcinoma cluster 4 antigen
CD24A
signal transducer CD24
true
A protein with core architecture consisting of a signal sequence, a Lectin C-type domain (Pfam:PF00059), 5 or 6 EGF-like domains (Pfam:PF00008, Pfam:PF09064, or Pfam:PF07645), a transmembrane region, and a small cytoplasmic region (36-51 amino acids).
thrombomodulin-like receptor
true
A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof.
p90
CD71
T9
TFRC
TfR
TfR1
Trfr
TR
transferrin receptor protein 1
true
A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain.
vascular endothelial growth factor receptor
true
A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human FLT3 gene or a 1:1 ortholog thereof.
CD135
FLK-2
FLT-3
FLT3
Fms-like tyrosine kinase 3
fetal liver kinase 2
stem cell tyrosine kinase 1
tyrosine-protein kinase FLT3
tyrosine-protein kinase receptor FLT3
tyrosine-protein kinase receptor flk-2
STK-1
STK1
receptor-type tyrosine-protein kinase FLT3
true
A thrombomodulin-like receptor that is a translation product of the human CD93 gene or a 1:1 ortholog thereof.
C1q/MBL/SPA receptor
C1qR
C1qR(p)
C1qRp
CD93
CDw93
cell surface antigen AA4
complement component 1 q subcomponent receptor 1
ly-68
lymphocyte antigen 68
matrix-remodeling-associated protein 4
Aa4
C1QR1
Ly68
MXRA4
complement component C1q receptor
true
A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human KIT gene or a 1:1 ortholog thereof.
CD117
KIT
SCFR
proto-oncogene c-Kit
tyrosine-protein kinase Kit
Sl
mast/stem cell growth factor receptor
true
A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof.
CD309
FLK-1
KDR
VEGFR-2
fetal liver kinase 1
kinase NYK
kinase insert domain receptor
protein-tyrosine kinase receptor flk-1
FLK1
vascular endothelial growth factor receptor 2
true
A protein that is the translation product of any of the LY6 genes (LY6A-LY6I).
ly-6-like protein
true
A KLRB1-like protein that is a translation product of the mouse Klrb1c gene or a 1:1 ortholog thereof.
CD161 antigen-like family member C
CD161c
Klrb1c
NK1.1
NKR-P1 40
NKR-P1.9
NKR-P1C
ly-55c
lymphocyte antigen 55c
natural killer cell surface protein P1-40
Ly55c
Nkrp1c
killer cell lectin-like receptor subfamily B member 1C
true
A ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof.
Ly6g
ly-6G
ly-6G.1
lymphocyte antigen 6G
true
A ly-6-like protein that is a translation product of the mouse Ly6a gene or a 1:1 ortholog thereof.
Ly6a
T-cell-activating protein
ly-6A.2/Ly-6E.1
stem cell antigen 1
Ly6
SCA-1
TAP
lymphocyte antigen 6A-2/6E-1
true
A protein that is a translation product of the mouse Ly76 gene or a 1:1 ortholog thereof.
Ly76
ter-119
ter119
lymphocyte antigen 76
true
A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof.
T-cell leukemia/lymphoma protein 5
TAL-1
TAL1
bHLHa17
class A basic helix-loop-helix protein 17
stem cell protein
SCL
TCL5
T-cell acute lymphocytic leukemia protein 1
true
An organic amino compound that is a polymer of amino acid chain components (unmodified amino-acid residues and/or modified amino-acid residues linked by peptide bonds or derivatives of such bonds.
peptide
polypeptide
amino acid chain
true
A protein that is composed of a long N-terminal extracellular domain, a transmembrane domain and a short cytoplasmic C-terminal domain. The N-terminal domain contains beta-propeller repeats (interrupted by an A domain in a subset of integrins alpha), while the C-terminal domain contains a GFFxR motif.
integrin alpha
true
region
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
primary structure of sequence macromolecule
sequence
region
true
supercontig
One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
supercontig
true
contig
A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
contig
true
sequence_assembly
A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
sequence_assembly
true
assembly
A region of the genome of known length that is composed by ordering and aligning two or more different regions.
assembly
true
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
portion of skin
region of skin
skin
skin region
skin zone
zone of skin
true
true
Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
anatomical tube
duct
tube
true
Major subdivision of an organism that protrudes from the body[DOS, CARO].
appendages
extremitaet
extremity
limbs/digits/tail
appendage
true
A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions.
lamina propria mucosa
lamina propria mucosae
tunica propria
lamina propria
true
The head is the anterior-most division of the body [GO].
head (volume)
adult head
cephalic area
head
true
A tubular structure that contains, conveys body fluid, such as blood or lymph.
vessel
true
A tubular structure that transports secreted or excreted substances.
anatomical duct
exocrine duct
exocrine gland duct
ducts
duct
true
Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
wall
wall of organ
organ wall
anatomical wall
true
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
AAO:0010825
AEO:0000003
BILA:0000003
CARO:0000003
EHDAA2:0003003
EMAPA:0
FBbt:00007001
FMA:305751
FMA:67135
GAID:781
HAO:0000003
MA:0003000
MESH:D000825
TAO:0000037
TGMA:0001823
VHOG:0001759
WBbt:0000100
XAO:0003000
ZFA:0000037
biological structure
connected biological structure
uberon
UBERON:0000061
biological structure
connected biological structure
anatomical structure
true
Anatomical structure that performs a specific function or group of functions [WP].
anatomical unit
body organ
element
organ
true
A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.
organ region with fixed fiat boundary
organ segment
segment of organ
organ subunit
true
A multicellular structure that is a part of an organ.
cardinal organ part
regional part of organ
organ part
true
Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts
respiratory tract
true
true
An section of a respiratory tract.
respiratory tract
subdivision of respiratory tract
proximo-distal subdivision of respiratory tract
true
true
Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
part of nervous system
regional part of nervous system
true
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
skeletal system subdivision
skeletal system part
subdivision of skeletal system
true
The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
surface (external) ectoderm
surface ectoderm
external ectoderm
true
true
An anatomical structure that develops from the endoderm and the mesoderm.
mixed endoderm/mesoderm-derived structure
true
true
The organs associated with producing offspring in the gender that produces spermatozoa.
genitalia of male organism
male genital system
male genitalia
male genitals
male organism genitalia
male organism reproductive system
reproductive system of male organism
male genital organ
male genital tract
male reproductive tract
systema genitale masculinum
male reproductive system
true
A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum.
morula (2-16 cells)
morula
true
A mass of cells that develop into the body of the embryo and some extraembryonic tissues
ICM
early embryoblast
embryoblast
embryoblastus; massa cellularis interna; pluriblastus senior
pluriblast
inner cell mass
true
the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta
trophoblast layer
massa cellularis externa
trophoblastus
trophoderm
trophoblast
true
A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc.
embryonic disc
embryonic shield
germinal disc
germinal disk
bilaminary embryonic disc
bilaminary germ disc
bilaminar disk
bilaminar disc
true
portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia]
cardiac neural crest complex
complexus cristae neuralis cardiacus
cardiac neural crest
true
true
true
The epithelial layer of the lung.
epithelial tissue of lung
epithelium of lung
lung epithelial tissue
pulmonary epithelium
lung epithelium
true
A tube in the respiratory system. Examples: bronchus, bronchiole, trachea.
segment of tracheobronchial tree
respiratory conducting tube
segment of tracheobronchial tree
tracheobronchial tree segment
respiratory tube
true
true
Structure derived from foregut that becomes a lung[GO].
gemma pulmonalis
gemma respiratoria
lung bud
primary lung bud
respiratory diverticulum
lung bud
true
true
anterior region of body
true
posterior region of body
true
membrane
membranous organ component
membranous layer
true
Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
bowel
intestinal tract
intestine
true
Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures
cloacal chamber
vent
cloaca
true
true
endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP].
cloaca
embryonic cloaca
true
the ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females
urogenital sinus
UGS
fetal UGS
sinus urogenitalis
primitive urogenital sinus
true
The pair of anatomical structures comprised of a left lung and right lung.
lungs
lungs pair
pulmones
set of lungs
pair of lungs
true
Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
apparatus respiratorius organ
breathing organ
organ of apparatus respiratorius
organ of respiratory system
respiratory organ
respiratory system organ
gas exchange organ
respiration organ
true
Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid.
acqua amnii
liquor amnii
amniotic fluid
true
A fluid that is composed of blood plasma and erythrocytes.
portion of blood
vertebrate blood
whole blood
blood
true
true
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
blood or blood analog
circulating fluid
haemolymphatic fluid
true
the thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected
amnios
amnion
true
true
true
Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
blastula embryo
blastosphere
blastula
true
An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching.
fetus
embryo late growth stage
embryo late stage
late embryo
true
The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin.
gastric gland
true
true
The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity).
digestive tract wall
wall of digestive tract
wall of gut
wall of alimentary tract
gut wall
true
A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm].
bowel mucosa gland
bowel mucosa of organ gland
bowel mucous membrane gland
bowel organ mucosa gland
gland of bowel mucosa
gland of bowel mucosa of organ
gland of bowel mucous membrane
gland of bowel organ mucosa
gland of intestinal mucosa
gland of intestine mucosa
gland of intestine mucosa of organ
gland of intestine mucous membrane
gland of intestine organ mucosa
gland of mucosa of bowel
gland of mucosa of intestine
gland of mucosa of organ of bowel
gland of mucosa of organ of intestine
gland of mucous membrane of bowel
gland of mucous membrane of intestine
gland of organ mucosa of bowel
gland of organ mucosa of intestine
glandula intestinalis
intestinal mucosa gland
intestine mucosa gland
intestine mucosa of organ gland
intestine mucous membrane gland
intestine organ mucosa gland
mucosa of bowel gland
mucosa of intestine gland
mucosa of organ of bowel gland
mucosa of organ of intestine gland
mucous membrane of bowel gland
mucous membrane of intestine gland
organ mucosa of bowel gland
organ mucosa of intestine gland
glandulae intestinales
intestinal gland
true
A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]
mucosa of organ
mucosa of organ part
mucosal region
mucous membrane
organ mucosa
region of mucosa
tunica mucosa
mucosa
true
functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues.
parenchyma
true
The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO].
blastocystis
blastula
blastocyst
true
true
An epithelial tissue layer that lines much of the urinary tract, including the renal pelvis, the ureters, the bladder, and parts of the urethra.
transitional epithelium
epithelium transitionale
transitional epithelium
uroepithelium
urothelium
true
true
The part of the hindlimb between pelvis and the knee, corresponding to the femur.
hind limb stylopod
hind limb stylopodium
hind propodium
hindlimb propodium
hindlimb stylopod
hindlimb stylopodium
proximal segment of free lower limb
stylopod of hind limb
stylopod of hindlimb
stylopod of lower limb
thigh
upper leg
femur
hindlimb stylopod
true
true
A mucosa that is part of a respiratory airway.
mucosa of organ of trachea
mucosa of organ of windpipe
mucosa of trachea
mucosa of windpipe
mucous membrane of trachea
mucous membrane of windpipe
organ mucosa of trachea
organ mucosa of windpipe
trachea mucosa
trachea mucosa of organ
trachea mucous membrane
trachea organ mucosa
tracheal mucous membrane
tunica mucosa (tracheae)
tunica mucosa tracheae
windpipe mucosa
windpipe mucosa of organ
windpipe mucous membrane
windpipe organ mucosa
tracheal mucosa
true
The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].
muscle system
muscle system of body
muscular system
musculature system
set of all muscles
set of muscles of body
vertebrate muscular system
muskelsystem
musculature of body
true
The outer covering of the calvaria. It is composed of several layers: SKIN; subcutaneous connective tissue; the occipitofrontal muscle which includes the tendonous galea aponeurotica; Loose connective tissue; and the pericranium (the PERIOSTEUM of the SKULL).
scalpus
scalp
true
true
A mucosa that is part of a bronchus [Automatically generated definition].
bronchi mucosa
bronchi mucosa of organ
bronchi mucous membrane
bronchi organ mucosa
bronchial trunk mucosa
bronchial trunk mucosa of organ
bronchial trunk mucous membrane
bronchial trunk organ mucosa
bronchus mucosa
bronchus mucosa of organ
bronchus mucous membrane
bronchus organ mucosa
mucosa of bronchi
mucosa of bronchial trunk
mucosa of bronchus
mucosa of organ of bronchi
mucosa of organ of bronchial trunk
mucosa of organ of bronchus
mucous membrane of bronchi
mucous membrane of bronchial trunk
mucous membrane of bronchus
organ mucosa of bronchi
organ mucosa of bronchial trunk
organ mucosa of bronchus
tunica mucosa bronchi
bronchial mucosa
true
true
A mesodermal signaling center of the hair follicle consisting of closely packed specialized mesenchymal fibroblasts. Framed by the enlarged bulb matrix in anagen.
dermal papillae
follicular papilla
dermal papilla cell
hair follicle dermal papilla
hair papilla
papilla corii
papilla dermatis
papilla dermis
papilla of corium
papillae dermis
skin papilla
dermal papilla
true
true
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
body fluid or substance
body substance
organism substance
portion of body substance
portion of organism substance
organism substance
true
Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
lumen
space
lumen space
anatomical spaces
anatomical space
true
Anatomical entity that has mass.
AAO:0010264
AEO:0000006
BILA:0000006
CARO:0000006
EHDAA2:0003006
FBbt:00007016
FMA:67165
HAO:0000006
TAO:0001836
TGMA:0001826
VHOG:0001721
uberon
UBERON:0000465
material anatomical entity
true
Anatomical entity that has no mass.
immaterial physical anatomical entity
immaterial anatomical entity
true
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
system
body system
connected anatomical system
organ system
anatomical systems
anatomical system
true
Anatomical structure that is an individual member of a species and consists of more than one cell.
TODO - split body and mc organism? body continues after death stage
organismal
AAO:0010026
AEO:0000191
BILA:0000012
BSA:0000038
BTO:0000042
CARO:0000012
EFO:0002906
EHDAA2:0003103
EHDAA2:0003191
EHDAA:1
EHDAA:9178
EMAPA:25765
EV:0100016
FBbt:00000001
FMA:256135
HAO:0000012
TADS:0000001
TAO:0001094
TGMA:0001832
VHOG:0000671
WBbt:0007833
XAO:0003004
ZFA:0001094
galen:Organism
ncithesaurus:Whole_Organism
multi-cellular organism
organism
whole organism
animal
uberon
Koerper
body
whole body
UBERON:0000468
organism
multi-cellular organism
animal
Koerper
body
whole body
whole organism
multicellular organism
true
The organs and associated structures associated with bearing offspring in a female animal.
female organism genitalia
female organism reproductive system
genitalia of female organism
reproductive system of female organism
female genital system
female genital tract
female genitalia
female genitals
female reproductive tract
gynaecological tissue
systema genitale femininum
female reproductive system
true
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
anatomic region
body part
body region
cardinal body part
organism subdivision
true
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
acellular anatomical structures
acellular anatomical structure
true
Anatomical group that has its parts adjacent to one another.
anatomical cluster
true
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
extra-embryonic structure
extraembryonic structures
extraembryonic tissue
extraembryonic structure
true
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
changed label and definition to reflect CARO2
AAO:0000607
AAO:0010054
AEO:0000043
BILA:0000043
CALOHA:TS-2090
CARO:0000043
EHDAA2:0003043
EMAPA:35868
FBbt:00007003
FMA:9637
HAO:0000043
MA:0003002
MESH:D014024
TAO:0001477
TGMA:0001844
UMLS:C0040300
VHOG:0001757
WBbt:0005729
XAO:0003040
ZFA:0001477
galen:Tissue
portion of tissue
tissue portion
simple tissue
uberon
UBERON:0000479
portion of tissue
tissue portion
simple tissue
tissue
true
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
multi-tissue structures
multi-tissue structure
true
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
epithelial tissue
portion of epithelium
epithelium
true
Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]
columnar epithelium
columnar epithlium
epithelium simplex columnare
simple columnar epithelium
simple columnar epithelia
simple columnar epithelium
true
true
Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]
stratified epithelium
laminated epithelium
multilaminar epithelium
true
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]
simple epithelium
unilaminar epithelia
unilaminar epithelium
true
Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid.
intercellular fluid
tissue fluid
interstitial fluid
true
Subdivision of trunk that lies between the head and the abdomen.
thorax
anterior subdivision of trunk
upper body
upper trunk
thoracic segment of trunk
true
true
The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.
abdominopelvic region
abdominopelvis
adult abdomen
belly
celiac region
abdomen
true
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
embryonic organism
developing organism
developmental tissue
embryo
true
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
embryonic tissue
germinal layer
primary germ layer
embryonic germ layer
embryonic germ layers
germ layer
true
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
embryonic ectoderm
ectoderm
true
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
entoderm
endoderm
true
The middle germ layer of the embryo, between the endoderm and ectoderm.
embryonic mesoderm
entire mesoderm
mesodermal mantle
mesoderm
true
An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
stomach chamber
anterior intestine
gaster
mesenteron
ventriculus
stomach
true
true
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
chambered heart
vertebrate heart
branchial heart
Herz@de
cardium
heart
true
true
true
true
true
Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
endocrine glandular system
endocrine system
systema endocrinum
endocrine system
true
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
encephalon
suprasegmental levels of nervous system
suprasegmental structures
synganglion
the brain
brain
true
true
The portion of the hindlimb that contains both the stylopod and zeugopod.
tetrapod leg
lower extremity
leg
true
true
Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified].
thigh bone
femoral bone
mesomere 1 of pevlic appendage
os femorale
os femoris
os longissimum
proximal metapterygial mesomere of pelvic appendage
proximal metapterygial mesomere of pelvic fin
femur
true
true
true
true
Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
articulation
joint
articular joint
joints
skeletal joint
true
Anatomical system that has as its parts the organs concerned with reproduction.
Geschlechtsorgan
animal reproductive system
genital system
genital tract
genitalia
organa genitalia
reproductive tissue
reproductive tract
systemata genitalia
reproductive system
true
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
gonada
gonads
gonad
true
A tube or collection of tubes in an animal from the ovaries to the outside of the body.
ovarian duct
ovarian tube
uterine tube
female reproductive tracts
oviducts
tuba uterina
tuba uterinae
tubular parts of female reproductive system
oviduct
true
true
the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth
uterus
true
The outer epithelial layer of the skin that is superficial to the dermis.
epidermis
skin
vertebrate epidermis
skin epidermis
true
true
Functional system which consists of structures involved in respiration.
apparatus respiratorius
respiratory system
Atmungssystem
apparatus respiratorius
systema respiratorium
respiratory system
true
An airway through which respiratory air passes in organisms.
airway
airways
respiratory airway
true
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
alimentary system
alimentary tract
gastrointestinal system
gut
digestive system
true
The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products..
excretory system
renal system
systema urinaria
systema urinarium
urinary system
urinary tract
renal or urinary system
renal/urinary system
renal system
true
organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
systema cardiovasculare
circulatory system
true
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
fat
fat tissue
fatty tissue
adipose
bodyfat
fatty depot
adipose tissue
true
A subdivision of the muscular system corresponding to a subdisivision of an organism.
muscle group
muscles set
musculature
musculi
set of muscles
set of skeletal muscles
muscle system
muscles
musculature system
musculature
true
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
neurological system
nerve net
systema nervosum
nervous system
true
The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
CNS
systema nervosum centrale
cerebrospinal axis
neuraxis
central nervous system
true
true
A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP].
saccus vitellinus
vesicula umbilicalis
yolk sac
true
true
true
Anterior subdivision of a digestive tract.
praeenteron
proenteron
foregut
true
Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
gullet
oesophagus
esophagus
true
true
true
Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO].
mesenteron
midgut
true
The caudalmost subdivision of a digestive tract.
metenteron
hindgut
true
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
bud
future organ
placode
primordia
rudiment
primordium
true
In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
neural primordium
presumptive central nervous system
tubus neuralis
neural tube
true
true
true
true
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
AAO:0010841
AEO:0000000
BILA:0000000
CARO:0000000
EHDAA2:0002229
FBbt:10000000
FBbt_root:00000000
FMA:62955
HAO:0000000
MA:0000001
TAO:0100000
TGMA:0001822
UMLS:C1515976
XAO:0000000
ZFA:0100000
uberon
UBERON:0001062
anatomical entity
true
A zone of skin that is part of a head [Automatically generated definition].
adult head zone of skin
head skin
head zone of skin
zone of skin of adult head
zone of skin of head
skin of head
true
An anatomical wall that is part of a esophagus [Automatically generated definition].
anatomical wall of esophagus
anatomical wall of gullet
anatomical wall of oesophagus
esophageal wall
esophagus anatomical wall
esophagus wall
gullet anatomical wall
gullet wall
oesophagus anatomical wall
oesophagus wall
wall of gullet
wall of oesophagus
wall of esophagus
true
Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO].
spine
backbone
vertebral column skeleton
columna vertebralis
dorsal spine
spinal column
vertebral region
vertebral column
true
Muscle tissue that consists primarily of skeletal muscle fibers.
skeletal muscle
skeletal muscle system
somatic muscle
skeletal muscle tissue
true
the layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between
anatomical wall of stomach
anatomical wall of ventriculus
gastric wall
stomach anatomical wall
stomach wall
ventriculus anatomical wall
ventriculus wall
wall of ventriculus
wall of stomach
true
The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel.
portal lobule
true
true
The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids.
liver acinus
portal acinus
hepatic acinus
true
true
A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder.
biliary tract
biliary tree
true
true
An artery that supplies the liver.
arteria hepatica propria
arteria hepatica
hepatic artery
true
The mucosal layer that lines the stomach.
gastric mucosa
gastric mucous membrane
mucosa of organ of stomach
mucosa of organ of ventriculus
mucosa of ventriculus
mucous membrane of stomach
mucous membrane of ventriculus
organ mucosa of stomach
organ mucosa of ventriculus
stomach mucosa
stomach mucosa of organ
stomach mucous membrane
stomach organ mucosa
tunica mucosa (gaster)
tunica mucosa gastricae
ventriculus mucosa
ventriculus mucosa of organ
ventriculus mucous membrane
ventriculus organ mucosa
Magenschleimhaut
tunica mucosa gastris
mucosa of stomach
true
Mucosal layer that lines the intestine.
bowel mucosa
bowel mucosa of organ
bowel mucous membrane
bowel organ mucosa
intestine mucosa
intestine mucosa of organ
intestine mucous membrane
intestine organ mucosa
mucosa of bowel
mucosa of intestine
mucosa of organ of bowel
mucosa of organ of intestine
mucous membrane of bowel
mucous membrane of intestine
organ mucosa of bowel
organ mucosa of intestine
tunica mucosa intestini
intestinal mucosa
true
The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad.
interlobular ductule
interlobular bile duct
true
An anatomical wall that is part of a intestine [Automatically generated definition].
anatomical wall of bowel
anatomical wall of intestine
bowel anatomical wall
bowel wall
intestinal wall
intestine anatomical wall
intestine wall
wall of bowel
bowel wall
wall of intestine
true
The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions.
girdle - pelvic
pelvic girdle
pelvic girdle region
true
true
The epithelial layer of the stomach .
epithelial tissue of stomach
epithelial tissue of ventriculus
epithelium of ventriculus
stomach epithelial tissue
stomach epithelium
ventriculus epithelial tissue
ventriculus epithelium
gastric epithelium
epithelium of stomach
true
true
true
true
Epithelial layer that lines the intestine.
bowel epithelial tissue
bowel epithelium
epithelial tissue of bowel
epithelial tissue of intestine
epithelium of bowel
epithelium of intestine
intestine epithelial tissue
villous epithelium
intestine epithelium
intestinal epithelium
true
true
true
true
A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel
trias hepatica
trias hepatica
portal triad
true
true
The functional units of the liver including the lobules.
hepatic parenchyma
liver parenchyme
parenchyma of liver
hepatic parenchyme
liver parenchyma
true
true
the tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule
canal of Herring
cholangiole
ductus interlobularis bilifer
canal of Hering
canals of Hering
duct of Herring
intrahepatic bile ductule
intralobular bile duct
true
true
The anus and surrounding regions. Encompasses both internal and external regions, where present
posterior
posterior end of organism
anal region
true
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.
skeleton system
set of all bones and joints
Skelettsystem
skeletal system
true
Subdivision of skeleton consisting of all skeletal elements in an hindlimb region.
bones of lower limb
free lower limb skeleton
hind limb skeleton
hind-limb skeleton
hindlimb skeleton
lower limb skeleton
ossa membri inferioris
set of bones of lower limb
skeleton of free lower limb
skeleton of lower limb
hindlimb skeleton
true
true
The hip region is located lateral to the gluteal region (i.e. the buttock), inferior to the iliac crest, and overlying the greater trochanter of the thigh bone. In adults, three of the bones of the pelvis have fused into the hip bone which forms part of the hip region. The hip joint, scientifically referred to as the acetabulofemoral joint (art. coxae), is the joint between the femur and acetabulum of the pelvis and its primary function is to support the weight of the body in both static (e.g. standing) and dynamic (e.g. walking or running) postures. [WP,modified].
hip region
regio coxae
coxa
hip
true
Skeletal element that is composed of bone tissue.
bone organ
bone
bones
bone element
true
A tube extending from the mouth to the anus.
gut
digestive tube
enteric tract
alimentary canal
alimentary tract
digestive canal
gut tube
digestive tract
true
The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]
lower respiratory tract
true
true
Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].
muscle
muscle organ
true
true
true
An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
arterial subtree
arterial tree organ part
arteries
arterial system
arterial vessel
artery
true
Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
venous subtree
venous vessel
venous tree organ part
vascular element
vena
venae
vein
true
The most anterior region the brain including both the telencephalon and diencephalon.
FB
prosencephalon
forebrain
true
the epithelial lining of the trachea which contains numerous ciliated cells
epithelial tissue of trachea
epithelial tissue of windpipe
epithelium of windpipe
trachea epithelial tissue
trachea epithelium
tracheal epithelium
windpipe epithelial tissue
windpipe epithelium
epithelium of trachea
true
An epithelium that is part of a respiratory bronchiole [Automatically generated definition].
bronchiolus respiratorius epithelial tissue
bronchiolus respiratorius epithelium
epithelial tissue of bronchiolus respiratorius
epithelial tissue of respiratory bronchiole
epithelium of bronchiolus respiratorius
respiratory bronchiole epithelial tissue
respiratory bronchiole epithelium
epithelium of respiratory bronchiole
true
An epithelium that lines a terminal bronchiole.
bronchiolus terminalis epithelial tissue
bronchiolus terminalis epithelium
epithelial tissue of bronchiolus terminalis
epithelial tissue of terminal bronchiole
epithelium of bronchiolus terminalis
epithelium of terminal bronchiole
terminal bronchiole epithelial tissue
terminal bronchiole epithelium
terminal bronchiole epithelium
true
The liquid component of blood, in which erythrocytes are suspended.
plasma
portion of plasma
blood plasm
portion of blood plasma
blood plasma
true
the epithelial layer that lines the luminal space of the esophagus
epithelial tissue of esophagus
epithelial tissue of gullet
epithelial tissue of oesophagus
epithelium of gullet
epithelium of oesophagus
esophageal epithelium
esophagus epithelial tissue
esophagus epithelium
gullet epithelial tissue
gullet epithelium
oesophagus epithelial tissue
oesophagus epithelium
epithelium of esophagus
true
true
A vessel through which blood circulates in the body.
vascular element
region of vascular tree organ
vascular tree organ region
vas sanguineum
blood vessel
true
true
the tubular intestinal glands found in the mucosal membranes
intestinal gland
Lieberkuhn crypt
Lieberkuhn gland
Lieberkuhn's gland
Lieberkuhn's glands
crypt of Lieberkuhn
crypt of Lieberkühn
crypts of Lieberkühn
follicles of lieberkuhn
intestinal crypt
intestinal crypts
lieberkuhn crypt
intestinal gland of Lieberkuhn
crypt of Lieberkuhn
true
organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
allantoic placenta
eutherian placenta
placenta
true
true
true
The upper layer of the dermis beneath the epidermis, composed of dense irregular connective tissue[ncit,modified].
corpus papillary
dermis papillary layer
papillary dermis
papillary layer
papillary layer of dermis
stratum papillare
stratum papillare (dermis)
stratum papillare corii
stratum papillare dermis
superficial dermis
dermal papillary layer
stratum papillare
papillary layer of dermis
true
true
A vein that conducts blood from the digestive organs, spleen, pancreas, and gallbladder to the liver[BTO].
portal venous tree organ part
portal vein
true
the deepest layer of the epidermis, which is composed of dividing stem cells and anchoring cells
Malpighian layer
rete Malphighii
rete Malpighii
stratum Malpighi
stratum basale
stratum germinosum
basal cell layer of epidermis
basal epidermal layer
epidermal basal stratum
epidermis stratum basale
stratum basalis of epidermis
stratum germinativum
stratum germinosum of epidermis
basal cell layer of skin
basal layer of epidermis
epidermis basal layer
epidermis sensorial layer
epidermis stratum germinativum
stratum basale of epidermis
true
true
true
An epithelium that is part of a bronchus [Automatically generated definition].
bronchi epithelial tissue
bronchi epithelium
bronchial epithelium
bronchial trunk epithelial tissue
bronchial trunk epithelium
bronchus epithelial tissue
bronchus epithelium
epithelial tissue of bronchi
epithelial tissue of bronchial trunk
epithelial tissue of bronchus
epithelium of bronchi
epithelium of bronchial trunk
epithelium of bronchus
true
Muscle tissue that contains fibers that are divided by transverse bands into striations.
striated muscle
striated muscle tissue
true
Respiration organ that develops as an oupocketing of the esophagus.
pulmo
lung
true
true
true
true
An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.
vascular network
vasculature
true
Anatomical structure that is part of an embryo.
developing embryonic structure
embryonic anatomical structure
developing structure
embryonale Struktur
embryonic structures
embryonic structure
true
An epithelium that is part of a bronchiole [Automatically generated definition].
bronchiolar epithelium
bronchiole epithelial tissue
bronchiole epithelium
epithelial tissue of bronchiole
epithelial tissue of lobular bronchiole
epithelium of lobular bronchiole
lobular bronchiole epithelial tissue
lobular bronchiole epithelium
epithelium of bronchiole
true
true
true
The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
vertebrate dermis
corium
cutis
dermis
true
true
true
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
hypoderm
vertebrate hypodermis
sub-tegumental tissue
subcutaneous tissue
subcutis
subtegumental tissue
superficial fascia
tela subcutanea
hypodermis
true
true
The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].
axial skeleton
post-cranial axial skeleton
postcranial axial skeleton
true
Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm].
appendicular skeleton
entire appendicular skeleton
paired fin skeleton
skeleton appendiculare
appendicular skeleton
true
The organ covering the body that consists of the dermis and epidermis.
entire skin
skin organ
entire integument
integument
integumental organ
pelt
skin
skin of body
true
true
true
Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.
thoracolumbar region
torso
trunk region
Rumpf
trunk
true
A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts.
free limb
limb sensu Vertebrata
pentadactyl limb
tetrapod limb
flipper
extremities
extremity
limb
true
A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts.
free lower limb
hind limb
hind-limb
hindlimb
inferior member
lower limb
membrum inferius
free part of lower limb
lower extremity
membrum inferius
pelvic appendage
hindlimb
true
true
An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
iecur
jecur
liver
true
true
true
true
true
Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]
right lung
true
Lung which consists of the left upper lobe and left lower lobe.[FMA]
left lung
true
the upper conducting airways of the lung; these airways arise from the terminus of the trachea
bronchi
bronchial trunk
bronchial tissue
bronchus
true
the conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching
lobular bronchiole
bronchioli
bronchiolus
bronchiole
true
the last conducting structure of non-respiratory bronchioles; after this point, the airways have alveoli in their walls
bronchiolus terminalis
bronchioli terminalis
terminal bronchiole tube
terminal bronchiole
true
A bronchiole that is the first segment of the respiratory zone.
bronchiolus respiratorii
bronchiolus respiratorius
respiratory bronchiole
true
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
hematolymphoid system
lymphomyeloid complex
haemolymphoid system
hemolymphoid system
true
The dermis, epidermis and hypodermis.
dermis plus epidermis plus hypodermis
integumentum commune
skin and subcutaneous tissue
skin plus hypodermis
the integument
Hautsystem@de
dermal system
dermoid system
skin
tegument
vertebrate integument
integument
true
Anatomical system that consists of the muscular and skeletal systems.
musculo-skeletal system
musculoskeletal system
true
Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]
articulatio synoviale
diarthroses
diarthrosis
diarthrosis joint
diarthrodial joints
synovial joint
true
Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree).
biliary apparatus
biliary tract
biliary system
true
Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.
mesodermal cluster
epimere
epimere mesoderm
epithelial somite
somites
somitic mesoderm
somitus
somite
true
true
Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia].
exocrine glandular system
exocrine system
true
The connecting cord from the developing embryo to the placenta.
chorda umbilicalis
funiculus umbilicalis
birth cord
connecting stalk
funiculus umbilicalis
yolk stalk
umbilical cord
true
A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP].
NC
crista neuralis
neural crest material
neural crest
true
true
true
Embryonic ectoderm that gives rise to nervous tissue.
neural ectoderm
neuroectoderm
epithelium tubi neuralis; neuroectoderma
neuaral ectoderm
presumptive central nervous system
ventral neurogenic region
neurectoderm
true
true
The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs.
lesser pelvis
pelvic region
pelvis
pelvis region
true pelvis
pelvic region of trunk
true
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas
ducted gland
glandula exocrina
exocrine gland
true
The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
male prostate
prostate
prostata
prostate gland
true
true
Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
ductless gland
glandula endocrina
ductless gland
glandulae endocrinae
endocrine gland
true
the soft tissue that fills the cavities of bones
medulla ossea
medulla ossium
medulla of bone
medullary bone
bone marrow
true
true
true
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]
Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]
MA also has set of connective tissues
AAO:0000098
BTO:0000421
CALOHA:TS-2009
EFO:0000952
EMAPA:35251
FMA:9640
GAID:100
MA:0000011
MAT:0000301
MESH:D003238
MIAA:0000301
OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA
TAO:0001641
UMLS:C0009780
VSAO:0000017
XAO:0001017
ZFA:0001632
galen:ConnectiveTissue
portion of connective tissue
textus connectivus
uberon
Bindegewebe
UBERON:0002384
portion of connective tissue
textus connectivus
Bindegewebe
connective tissue
true
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
muscular tissue
portion of muscle tissue
textus muscularis
muscle tissue
true
true
Anatomical system that is involved in the production of hematopoietic cells.
haematological system
haemopoietic system
organa haemopoietica
Blutbildungssystem
haematopoietic system
hematological system
hematolymphoid system
hemopoietic system
hematopoietic system
true
true
Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP].
lympha
lymph
true
Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine.
bile tube
biliary duct
gall duct
hepatic duct
bile duct
true
true
Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.
immune system
true
The ossified form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column.
vertebra bone
vertebrae
vertebra
true
true
true
Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
integumentary system
body surface
dermal system
external covering of organism
integumentum commune
organism surface
surface
integumental system
true
The abdominal segment of the torso.
abdomen/pelvis/perineum
lower body
lower trunk
lumbar region
abdominal segment of trunk
true
true
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.
cartilage tissue
cartilaginous tissue
chondrogenic tissue
cartilage
cartilages
portion of cartilage tissue
cartilage tissue
true
The part of the digestive system that contains the liver and the biliary system
hepaticobiliary system
liver and biliary system
liver/biliary system
hepatobiliary system
true
A bone that is part of a limb [Automatically generated definition].
bone of extremity
bone of limb
free limb bone
limb bone
true
true
true
The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP].
lymphatic system
lymphatic circulatory system
lymphatic drainage system
systema lymphoideum
lymphoid system
true
A mucosa that is part of a esophagus [Automatically generated definition].
esophageal mucosa
esophageal mucous membrane
esophagus mucosa
esophagus mucous membrane
lamina muscularis mucosae oesophageae
mucosa of esophagus
mucosa of oesophagus
mucous membrane of esophagus
mucous membrane of oesophagus
oesophageal mucosa
oesophagus mucosa
oesophagus mucous membrane
tunica mucosa esophagi
tunica mucosa oesophageae
tunica mucosa oesophagi
muscularis mucosae of oesophagus
tunica mucosa oesophagi
esophagus mucosa
true
The proximal free limb segment. Includes as parts the stylopod skeleton.
proximal part of limb
propodium
proximal free limb segment
stylopodial limb segment
stylopodium
proximal segment of free limb
stylopod
true
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.
calcium tissue
osseous tissue
osteogenic tissue
mineralized bone tissue
bone
portion of bone tissue
bone tissue
true
Long bone is a limb bone that is subcylindrical and has a shaft with periosteum separating the ends of the bones. Long bones are present only in the limbs[VSAO:wd].
os longum
long bone
true
Replacement bone that forms within cartilage.
ossified chondrogenic bone
cartilaginous bone
endochondral bones
endochondral bone
true
true
the thick fibrous membrane that closely invests the entire surface of a bone except the articular cartilage at synovial joints
periosteum
true
A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles.
free limb segment
segment of limb
subdivision of limb
extremity part
limb region
region of limb
limb segment
true
an organ that functions as a secretory or excretory organ
glandular organ
Druese
glandula
gland
true
In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]
epiblast
blastocyst
ectoblast
epiblastus
primitive ectoderm
epiblast (generic)
true
Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia.
anatomical structure of brain
biological structure of brain
brain anatomical structure
brain biological structure
brain part
neuraxis segment
neuroanatomical region
segment of brain
regional part of brain
true
true
The portion of neural plate anterior to the mid-hindbrain junction.
anterior neural plate
pre-chordal neural plate
true
true
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.
segmental plate
unsegmented paraxial mesoderm
PSM
presumptive somite mesoderm
somitogenic mesoderm
somitomeric mesoderm
unsegmented mesenchyme
presomitic mesoderm
true
Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].
ventral lateral plate mesoderm
blood islands
VBI
caudal hematopoietic tissue
posterior ICM
posterior blood island
ventral blood island
blood island
true
The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads.
IM
intermediate mesenchyme
intermediate plate
intermediate plate mesoderm
mesenchyma intermedium
intermediate mesoderm
true
A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]
lamina neuralis
presumptive central nervous system
neural plate
true
true
true
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]
paraxial mesenchyme
somitic mesoderm
mesoderma paraxiale
paraxial mesoderm
true
true
true
anterior neural tube
true
Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].
LPM
lateral mesoderm
lateral plate
lateral plate mesenchyme
mesoderma laminae lateralis
lateral plate mesoderm
true
true
true
true
A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.
myomeres
muscle plate
myomere
myotome region
myotomes
myotomus
myotome
true
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone.
cardiac field
fused heart primordium
heart primordium
true
Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].
sclerotomes
sclerotomus
sclerotome
true
true
Gonochoristic organism that can produce female gametes.
female human body
female
female organism
true
Gonochoristic organism that can produce male gametes.
male human body
male
male organism
true
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
anatomical surface feature
surface feature
surface region
surface structures
surface structure
true
Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
organ
compound organ
true
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO].
mesenchymal tissue
mesenchyme tissue
portion of mesenchymal tissue
portion of mesenchyme tissue
mesenchyma
mesenchyme
true
the outermost extraembryonic membrane
chorion (vertebrates)
embryonic chorion
fetal chorion
uterine chorion
chorion frondosum
chorionic sac
chorion
true
true
true
The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph].
cartilaginous trachea
vertebrate trachea
windpipe
tracheal tubule
trachea
true
An organ involved in reproduction
genital organ
reproductive system organ
sex organ
genitalia
reproductive organ
true
true
amnion ectoderm
amnionic ectoderm
amnion epithelium
amniotic ectoderm
true
true
true
true
An endoderm that is part of a foregut [Automatically generated definition].
foregut endoderm
endoderm of foregut
true
true
true
A mesenchyme that is part of a amnion.
amnion mesenchyme
amnion mesoderm
amnionic mesoderm
mesenchyme of amnion
amnionic mesenchyme
amnionic mesoderm
amniotic mesoderm
true
true
true
A mesenchyme that is part of a chorion.
chorion mesenchyme
chorion mesoderm
chorionic mesenchyme
mesenchyme of chorion
mesenchyme of chorion (vertebrates)
chorionic mesenchyme
true
true
true
A gland that is part of a foregut [Automatically generated definition].
foregut gland
gland of foregut
true
A layer of epithelial cells on the surface of the mucosa.
lamina epithelialis mucosa
lamina epithelialis mucosae
epithelium of mucosa
true
An epithelium that is part of a hindgut [Automatically generated definition].
epithelial tissue of hindgut
hindgut epithelial tissue
hindgut epithelium
epithelium of hindgut
true
A extraembryonic structure that develops_from a ectoderm and is part of a chorion.
chorion ectoderm
chorion epithelium
chorionic epithelium
chorionic ectoderm
true
A gland that is part of a digestive tract [Automatically generated definition].
digestive tract gland
gland of digestive tract
gland of lower gastrointestinal tract
gut gland
lower gastrointestinal tract gland
gland of digestive tract
true
true
A gelatinous substance within the umbilical cord, largely made up of mucopolysaccharides (hyaluronic acid and chondroitin sulfate). It also contains some fibroblasts and macrophages. It is derived from Extra Embryonic Mesoderm[WP]
Wharton's jelly
umbilical cord mesenchyme
mesenchyme of umbilical cord
true
true
true
A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle)
bone of hind limb
bone of hindlimb
bone of inferior member
bone of lower extremity
bone organ of hind limb
bone organ of hindlimb
bone organ of lower extremity
hind limb bone
hind limb bone organ
hindlimb bone organ
hindlimb bone
true
true
true
A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.
arterial blood vessel
true
A long bone that is part of a limb [Automatically generated definition].
long bone of limb
limb long bone
true
true
A long bone that is part of a hindlimb [Automatically generated definition].
hind limb long bone
inferior member long bone
long bone of hind limb
long bone of hindlimb
long bone of inferior member
long bone of lower extremity
lower extremity long bone
hindlimb long bone
true
true
Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct.
bile duct extrahepatic part
extrahepatic biliary system
extrahepatic bile duct
true
Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct.
bile duct intrahepatic part
intrahepatic biliary system
intrahepatic bile duct
true
Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
nerve tissue
nervous tissue
portion of neural tissue
neural tissue
true
A region of the fetal urogenital sinus epithelium destined to become the prostate[GO].
prostate ductal progenitor
prostatic bud
prostate gland bud
prostate primordium
prostate bud
true
true
A bone that is part of a hindlimb stylopod [Automatically generated definition].
femur
upper leg bone
true
Mesenchyme that is part of a developing hindlimb [Automatically generated definition].
hind limb mesenchyme
inferior member mesenchyme
lower extremity mesenchyme
mesenchyme of hind limb
mesenchyme of hindlimb
mesenchyme of inferior member
mesenchyme of lower extremity
hindlimb mesenchyme
true
A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum.
embryological hepatic plate
primordium of the liver
hepatic plate
liver bud
liver endoderm
liver primordium
true
true
true
true
true
Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
epithelial or endothelial tube
epithelial tube
true
true
A blood vessel that carries blood from the capillaries toward the heart
segment of venous tree organ
venous tree organ segment
venous blood vessel
true
A duct that is part of a digestive system [Automatically generated definition].
duct of digestive system
duct of gastrointestinal system
gastrointestinal system duct
digestive system duct
true
An epithelium that lines the lumen of the digestive tract.
digestive tract epithelial tissue
epithelial tissue of digestive tract
epithelial tissue of gut
epithelium of digestive tract
epithelium of gut
gastrodermis
gut epithelial tissue
gut epithelium
alimentary tract epithelium
digestive tract epithelium
true
Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction.
genitalia gland
gland of genitalia
gland of reproductive system
reproductive gland
reproductive system gland
sex gland
reproductive gland
true
true
A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.
cutis plate
dermatomal mesenchyme
epimere mesoderm
mesenchyma dermatomiale
dermatome
true
Any tube, opening or passage that connects two distinct anatomical spaces.
foramen
foramina
opening
ostia
ostium
anatomical conduit
true
An anatomical structure that develops (entirely or partially) from the endoderm.
endoderm-derived structure
true
An anatomical structure that develops (entirely or partially) from the mesoderm.
mesodermal derivative
mesoderm-derived structure
true
An anatomical structure that develops (entirely or partially) from the ectoderm.
ectodermal deriviative
ectoderm-derived structure
true
Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.
urogenital system
GU tract
UG tract
Urogenitalsystem
genito-urinary system
genitourinary tract
urogenital tract
genitourinary system
true
true
The first recognizable structure derived from the heart field
myocardial plate
cardiac crescent
cardiogenic crescent
heart rudiment
cardiogenic plate
true
A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.
first heart field
primary heart field
FHF
PHF
heart field
primary heart field
true
true
true
true
An epithelial tube that will give rise to the mature heart.
embryonic heart tube
endocardial heart tube
endocardial tube
heart tube
true
true
true
A cardiac chamber surrounds an enclosed cavity within the heart
chamber of heart
heart chamber
cardiac chamber
true
true
A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG].
transverse septum
septum transversum
true
The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals
internal genitalia
internal genitals
internal reproductive organ
internal sex organ
internal genitalia
true
A portions of the gut that is derived from endoderm.
endodermal gut
gut endoderm
endodermal part of digestive tract
true
true
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.
set of all bones
set of bones of body
skeleton
true
The bilaminar epithelium formed from the myotome and dermatome.
dermamyotome
dermomyotomes
dermomyotome
true
true
A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.
heart cone
rudimentary heart
heart rudiment
true
A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG].
allantoic bud
allantois
true
true
outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition
trophectoderm
true
true
An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
limb buds
limbbud
gemmae membrorum
limb bud
true
multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP].
apical epidermal ridge
AER
crista ectodermalis apicalis
apical ectodermal ridge
true
An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
limb - fin bud
paired appendage bud
paired limb/fin bud
paired limb/fin bud
true
true
A bone that is part of an appendage [Automatically generated definition].
appendage bone
bone of appendage
bone of free segment of appendicular skeleton
bone of free limb or fin
true
true
The collection of all skeletal elements in an individual limb.
free limb skeleton
limb skeleton
set of bones of limb
skeleton of limb
true
true
Anatomical system that has as its parts the heart and blood vessels.
CV system
Herz und Gefaesssystem
cardiovascular system
true
A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.
lymphatic trunks and ducts
lymphatic vasculature
lymphatic vessel network
lymphatic vessels set
set of lymphatic vessels
trunci et ductus lymphatici
lymph vessels
lymph vasculature
true
true
A vascular network consisting of blood vessels.
blood vascular network
set of blood vessels
blood system
blood vessel system
blood vessels
blood vasculature
true
The part of the cardiovascular system consisting of all arteries.
arterial system
true
The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions.
vein system
venous system
true
the polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein
hepatic lobule
lobuli hepatici
lobulus hepaticus
lobules of liver
lobuli hepatis
liver lobule
true
true
An appendage that is part of an appendage girdle complex.
girdle-associated appendage
limb or fin
limb/fin
pectoral or pelvic appendage
pelvic/pectoral appendage
jointed paired lateral appendage
paired appendage
paired limb/fin
true
Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues.
posterior appendage
hindlimb/pelvic fin
pelvic appendage
pelvic limb/fin
posterior limb/fin
posterior paired appendage
pelvic appendage
true
The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].
embryo plus adnexa
conceptus
true
Organism at the gastrula stage.
gastrula embryo
blastocystis trilaminaris
tri-laminar disc
tri-laminar disk
trilaminar blastocyst
trilaminar blastoderm
trilaminar disc
trilaminar disk
trilaminar germ
gastrula
true
A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]
skeletal tissue
true
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
skeletal element
true
Anatomical system that consists of all the joints of the body.
joint system
set of all joints of body
set of all joints
set of joints of body
articular system
true
the mucous membrane lining the respiratory tract
apparatus respiratorius mucosa
apparatus respiratorius mucosa of organ
apparatus respiratorius mucous membrane
mucosa of apparatus respiratorius
mucosa of organ of apparatus respiratorius
mucosa of organ of respiratory system
mucosa of respiratory system
mucous membrane of apparatus respiratorius
mucous membrane of respiratory system
respiratory system mucosa of organ
respiratory system mucous membrane
laryngeal mucous membrane
respiratory mucosa
respiratory tract mucosa
respiratory system mucosa
true
A mucosa that is part of a gastrointestinal system.
digestive tract mucosa
gut mucosa
gut mucuous membrane
mucosa of gut
gastrointestinal system mucosa
true
the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi
epithelial tissue of respiratory tract
epithelium of respiratory tract
respiratory tract epithelial tissue
airway epithelium
respiratory epithelium
respiratory tract epithelium
true
true
true
An epithelium that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius epithelial tissue
apparatus respiratorius epithelium
epithelial tissue of apparatus respiratorius
epithelial tissue of respiratory system
epithelium of apparatus respiratorius
epithelium of respiratory system
respiratory system epithelial tissue
respiratory system epithelium
true
An epithelium that is part of a digestive system [Automatically generated definition].
digestive system epithelial tissue
digestive system epithelium
epithelial tissue of digestive system
epithelial tissue of gastrointestinal system
epithelium of digestive system
epithelium of gastrointestinal system
gastrointestinal system epithelial tissue
gastrointestinal system epithelium
true
An epithelium that is part of a lower respiratory tract [Automatically generated definition].
epithelial tissue of lower respiratory tract
epithelium of lower respiratory tract
lower respiratory tract epithelial tissue
lower respiratory tract epithelium
true
Layer of lateral plate mesoderm that forms the future body wall - underlies the ectoderm[WP].
outer layer of lateral plate mesoderm
parietal mesoderm
somatic mesoderm
somatic layer of lateral plate mesoderm
true
Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].
visceral mesoderm
inner layer of lateral plate mesoderm
splanchnic mesoderm
splanchnic layer of lateral plate mesoderm
true
A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP].
somatopleure
true
The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra
UGE
epithelium of urogenital sinus
urogenital sinus epithelium
true
Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts.
joint
articulation
true
The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum.
upper GI tract
upper gastrointestinal tract
upper digestive tract
true
hepatic diverticulum
biliary bud
true
true
true
true
A proximal-distal subdivision of the digestive tract.
alimentary system subdivision
intestinal tract
segment of intestinal tract
subdivision of alimentary system
subdivision of digestive tract
true
A part of a wall of an organ that forms a layer.
organ component layer
true
A mucosa that is part of a bronchiole [Automatically generated definition].
bronchiole mucosa
bronchiole mucosa of organ
bronchiole mucous membrane
bronchiole organ mucosa
lobular bronchiole mucosa
lobular bronchiole mucosa of organ
lobular bronchiole mucous membrane
lobular bronchiole organ mucosa
mucosa of lobular bronchiole
mucosa of organ of bronchiole
mucosa of organ of lobular bronchiole
mucous membrane of bronchiole
mucous membrane of lobular bronchiole
organ mucosa of bronchiole
organ mucosa of lobular bronchiole
mucosa of bronchiole
true
The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.
neural groove
true
One of the two elevated edges of the neural groove[GO,MP].
medullary fold
neural fold
true
true
true
true
true
A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].
neural tube rod
neural rod
true
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
musculus
muscle
muscle element
muscle structure
true
A bud is a protrusion that forms from an epithelial sheet by localized folding.
epithelial bud
true
Any anatomical structure that is part of the reproductive system.
reproductive system element
reproductive system structure
reproductive structure
true
An epithelial sheet bent on a linear axis.
epithelial fold
true
An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
abdomen organ
abdomen element
true
An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.
abdominal segment organ
abdominal segment element
true
An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
trunk organ
trunk region element
true
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
thoracic cavity organ
thoracic cavity element
true
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
upper body organ
thoracic segment organ
true
Mesenchyme that is part of a developing hindlimb stylopod [Automatically generated definition].
upper leg mesenchyme
true
Mesenchyme that is part of a developing trunk.
trunk and cervical mesenchyme
trunk mesenchyme
true
true
A portion of tissue that is part of an embryo.
portion of embryonic tissue
developing tissue
embryonic tissue
true
Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo.
extra-embryonic tissue
extraembryonic tissue
true
A sex gland that is part of a male reproductive system.
accessory sex gland
male reproductive gland
true
The part of the digestive system that excludes the hepatobiliary system.
GI tract
alimentary system
alimentary tract
gastro-intestinal system
gastrointestinal (GI) tract
gastrointestinal system
gastrointestinal tract
alimentary part of gastrointestinal system
true
A limb bud that develops into a hindlimb.
hind limb bud
posterior limb bud
leg bud
limb bud - hindlimb
hindlimb bud
true
true
A limb bud that develops into a hindlimb or pelvic fin.
hindlimb/pelvic fin bud
pelvic fin bud
pelvic fin buds
pelvic appendage bud
true
developing structure
developmental structure
developmental tissue
developing anatomical structure
true
Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA].
VNC
enteric neural crest
post-otic neural crest
vagal neural crest
true
true
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
primitive heart tube
early primitive heart tube
primitive heart tube
true
true
Portion of tissue that gives rise to the immature gonad.
future gonad
gonadal primordium
primitive gonad
undifferentiated gonad
immature gonad
gonad primordium
true
A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum.
lateral diverticula
lung diverticulum
lung endoderm
lung primordium
true
Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo.
extraembryonic membrane
true
.
extra-embryonic mesoderm
extraembryonic mesenchyme
extraembryonic mesoderm
true
true
true
A acellular anatomical structure that is the bounding layer of a anatomical structure.
acellular membrane
true
An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.
basement membrane of connective tissue
membrana basalis
basement membrane
basement membrane of epithelium
true
fetal uterus
embryonic uterus
true
In the circulatory system of animals, a portal venous system occurs when a capillary bed drains into another capillary bed through veins, without first going through the heart. Both capillary beds and the blood vessels that connect them are considered part of the portal venous system. They are relatively uncommon as the majority of capillary beds drain into veins which then drain into the heart, not into another capillary bed. Portal venous systems are considered venous because the blood vessels that join the two capillary beds are either veins or venules. Examples of such systems include the hepatic portal system and the hypophyseal portal system. Unqualified, 'portal venous system' often refers to the hepatic portal system. For this reason, 'portal vein' most commonly refers to the hepatic portal vein[WP].
portal venous system
portal system
true
A delimited region of dense mesenchyme within looser mesenchyme.
mesenchyme condensation
developing mesenchymal condensation
true
true
Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes.
cartilage condensation
cartilagenous condensation
chondrogenic condensation
cartilaginous condensation
true
A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts.
pre-chondrogenic condensation
precartilage condensation
precartilagenous condensation
prechondrogenic condensation
pre-cartilage condensation
true
true
A bone that is part of the region of the hindlimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia. Counter-examples: any pes phalanx
leg bone
true
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]
endoderm-derived epithelium
endoepithelium
endo-epithelium
true
true
Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
skeleton axiale
axial skeleton plus cranial skeleton
true
A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong].
amnionic fold
amniotic fold
true
A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions).
multi-limb segment region
true
A femur endochondral element that is composed primarily of a pre-cartilage condensation.
femoral pre-cartilage condensation
femur pre-cartilage condensation
true
true
true
true
An anatomical junctions that overlaps the foregut and midgut.
foregut-midgut junction
true
The embryonic precursor of the brain.
brain rudiment
presumptive brain
encephalon
embryonic brain
future brain
true
A presumptive structure that has the potential to develop into a forebrain.
future prosencephalon
presumptive forebrain
presumptive prosencephalon
prosencephalon
future forebrain
true
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
fluid
body fluid
bodily fluid
true
An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system.
lymphatic system
lymphatic tree system
lymporeticular system
lymphatic part of lymphoid system
true
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
anterior part of foregut
pharyngeal tube
pharynx
true
Presumptive structure of the blastula that will develop into endoderm.
presumptive endoderm
true
future blood
presumptive blood
true
Portion of embryonic tissue determined by fate mapping to become a structure.
future structure
presumptive structures
presumptive structure
true
Presumptive structure of the blastula that will develop into ectoderm.
presumptive epidermis
presumptive ectoderm
true
Presumptive structure of the blastula that will develop into mesoderm.
presumptive mesoderm
true
A sheet of extracellular matrix.
aponeuroses
aponeurotic
aponeurosis
true
The galea aponeurotica (epicranial aponeurosis, aponeurosis epicranialis) is a tough layer of dense fibrous tissue which covers the upper part of the cranium; behind, it is attached, in the interval between its union with the Occipitales, to the external occipital protuberance and highest nuchal lines of the occipital bone; in front, it forms a short and narrow prolongation between its union with the Frontales. On either side it gives origin to the Auriculares anterior and superior; in this situation it loses its aponeurotic character, and is continued over the temporal fascia to the zygomatic arch as a layer of laminated areolar tissue. It is closely connected to the integument by the firm, dense, fibro-fatty layer which forms the superficial fascia of the scalp: it is attached to the pericranium by loose cellular tissue, which allows the aponeurosis, carrying with it the integument to move through a considerable distance.
aponeurosis epicranialis
aponeurosis of epicranius
epicranial aponeurosis
epicranius aponeurosis
galea aponeurotica
cranial aponeurosis
epicranial aponeurosis
galea aponeurosis
galea aponeurotica; aponeurosis epicranialis
galeal aponeurosis
epicranial aponeurosis
true
An epithelium that is composed primarily of secretory cells.
glandular epithelium
true
Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand.
loose areolar connective tissue
areolar tissue
loose connective tissue
areolar connective tissue
true
The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus.
rectum
rectal part of digestive tract
terminal section of digestive tract
terminal part of digestive tract
true
A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands.
epithelium of gastric gland
gastric gland epithelium
stomach glandular epithelium
true
true
Any gland that is part of the digestive system.
digestive gland
digestive system gland
true
true
Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA]
glandular columnar epithelium
true
true
stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region.
stomach glandular region glandular mucous membrane
stomach glandular region mucosa
true
The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA].
vascular cord
true
The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO].
cardiogenic splanchnopleure
cardiac mesoderm
cardiogenic mesoderm
cardiogenic region
heart primordia
cardiogenic splanchnic mesoderm
true
true
Organism at the cleavage stage.
cleaving embryo
true
future digestive tract
future digestive tube
future gut
primitive gut
embryonic digestive tube
primordial digestive tube
primordial gut
presumptive gut
true
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
dorsal tube
heart
adult heart
primary circulatory organ
true
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.
presumptive central nervous system
neural keel
true
The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells.
arbor tracheobronchialis
tracheobronchial system
tracheobronchial tree
true
true
true
The collection of all skeletal elements in a pelvic appendage region.
pelvic appendage skeleton
true
A presumptive structure that has the potential to develop into a presomitic mesoderm.
presumptive segmental plates
presumptive segmental plate
true
A presumptive structure that has the potential to develop into a neural plate.
prospective neuroectoderm
prospective vegetal ectoderm
presumptive neural plate
true
The part of the blastula that has the potential to develop into a paraxial mesoderm.
future paraxial mesenchyme
future paraxial mesoderm
presumptive paraxial mesoderm
true
The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO].
epidermis
epidermis (sensu Metazoa)
outer epidermal layer
outer epithelial layer
hypoderm
hypodermis
outer epithelium
true
true
Outermost layer of cells surrounding the embryo.
EVL
enveloping layer
enveloping layer of ectoderm
true
true
true
An epithelial tube that is open at one end only.
epithelial sac
true
true
An epithelial tube open at both ends that allows fluid flow.
epithelial tube open at both ends
true
A closed epithelium with a lumen.
epithelial vesicle
true
Mesenchyme with little extracellular matrix.
dense mesenchyme tissue
true
Mesenchymal cells that are migrating.
migrating mesenchyme population
true
Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]
ciliated columnar epithelium
true
true
Epithelium bearing vibratile cilia on the free surface.
ciliated epithelium
true
An anatomical structure that connects two structures
junction
anatomical junction
anatomical junction
true
Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.
field
developmental field
future organ
organ field
anlage
true
true
Anatomical system that consists of all blood and lymph vessels.
Gefaesssystem@de
vascular system
true
A bridge of mesoderm connecting the caudal end of the young embryo with the trophoblastic tissues; the precursor of the umbilical cord.
connecting stalk
true
The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.
cephalic area
cephalic part of animal
cephalic region
head and neck
head or neck
craniocervical region
true
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
girdle
girdle region
fin girdle
fin girdle region
limb girdle
limb girdle region
appendage girdle region
true
Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature.
pelvic girdle skeleton
skeletal parts of pelvic girdle
skeleton of pelvic girdle
pelvic girdle
pelvic girdle skeleton
true
true
Skeletal element that is composed of cartilage tissue and may be permanent or transient.
cartilage organ
cartilaginous element
chondrogenic element
cartilage
cartilage element
true
The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid.
os irregulare
os irregulare
irregular bone
true
bone of hip region
true
An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers
embryonic epiblast
inner cell mass derived epiblast
true
A limb segment that is part of a hindlimb.
free lower limb segment
free lower limb subdivision
segment of free lower limb
subdivision of free lower limb
lower limb segment
true
An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts.
liver diverticulum
diverticulum hepaticum
hepatic diverticulum
true
true
true
true
true
liver bud
true
true
true
true
The part of the airway consisting of a respiratory bronchiole and all of its branches
acinus pulmonaris
arbor alveolaris
lobulus pulmonis primarius
primary pulmonary lobule
respiratory lobule
pulmonary acinus
true
respiratory primordium
true
Sum total of mesenchyme in the embryo.
entire embryonic mesenchyme
true
An epithelium that is part of a foregut-midgut junction.
epithelium of foregut-midgut junction
true
true
true
An endoderm that is part of a anal region.
anal membrane endodermal component
true
true
An endoderm that is part of a foregut-midgut junction.
endoderm of foregut-midgut junction
true
region of trunk
trunk subdivision
subdivision of trunk
true
trunk and cervical paraxial mesenchyme
trunk paraxial mesenchyme
trunk paraxial mesoderm
true
The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells.
limb mesoderm
limb mesenchyme
true
The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form.
acinus
acini
glandular acinus
true
An epithelium that is part of a embryonic cloaca.
cloacal epithelium
embryonic cloacal epithelium
true
true
true
A specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop.
prostate primordium
prostate field
true
true
true
true
Branch or outpocketing of the digestive tract.
diverticulum of gut
intestinal pouch
digestive tract diverticulum
true
true
pouch
diverticulum
sac
true
A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland.
gastric zone
region of stomach
section of stomach
zone of stomach
true
ALPM
anterior lateral plate mesoderm
true
true
lobulus
lobule
true
An anatomical structure that has more than one cell as a part.
CARO:0010000
FBbt:00100313
multicellular structure
uberon
UBERON:0010000
multicellular structure
multicellular anatomical structure
true
An organ of the digestive tract that is capable of retaining and storing food
food storage organ
true
Mesenchyme that has the potential to develop into a dermis.
future dermis
true
A femur endochondral element that is composed primarily of cartilage tissue.
femoral cartilage condensation
femur cartilage element
true
true
true
true
Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male.
male accessory gland
male accessory reproductive gland
male accessory sex gland
true
An anatomical structure that has some part that develops from the neural crest.
structure with developmental contribution from neural crest
true
germ layer / neural crest
true
true
Mesenchyme that is part of a extraembryonic membrane.
extraembryonic membrane mesenchyme
true
true
true
A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification.
endochondral replacement element
endochondral element
true
The smallest anatomical unit of the lung, measuring 0.50 to 2.00 cm in diameter. Each lobule is composed of 4-8 terminal bronchioles and their distal alveolar ducts and sacs. The lobules are separated by fibrous interlobular septa.
lobulus pulmonis
pulmonary lobule
true
true
Epithelium composed of cells that develops from the ectoderm[FMA,modified].
ectoderm-derived epithelium
ecto-epithelium
true
true
Mesenchyme that develops_from a somatopleure.
mesenchyme from somatopleure
true
true
true
A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels.
pseudostratified columnar epithelium
true
Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile.
epithelium pseudostratificatum columnare ciliatum (trachea et bronchi)
pseudostratified ciliated columnar epithelium
true
true
An appendage segment that is part of a limb/fin.
limb/fin segment
paired limb/fin segment
true
An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
appendage complex
appendage-girdle complex
appendage/girdle complex
girdle plus limb or fin
limb
appendage girdle complex
true
true
Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle.
pelvic appendage/girdle complex
pelvic girdle plus pelvic limb or fin
pelvic girdle plus posterior limb or fin
lower limb
lower limb and pelvic girdle
lower limb and pelvis
pelvic complex
true
Skeletal subdivision that is a segment of the limb skeleton.
limb skeleton subdivision
true
The subdivision of the skeleton of either the pectoral or pelvic girdle.
skeleton of girdle
girdle skeleton
true
A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle).
bone of extended limb/fin region
limb bone
bone of appendage girdle complex
true
A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle.
hindlimb bone
bone of pelvic complex
true
A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg.
appendage segment
appendicular segment
subdivision of organism along appendicular axis
true
A skeletal element that is part of a limb and composed of cartilage tissue.
limb cartilage element
true
true
A skeletal element that is part of a limb and composed of pre-cartilage tissue.
limb bone pre-cartilage condensation
true
A cartilaginous condensation that has the potential to develop into a hindlimb bone.
hindlimb cartilage condensation
hindlimb cartilage element
true
true
A pre-cartilage condensation that has the potential to develop into a hindlimb bone.
hindlimb pre-cartilage condensation
hindlimb pre-cartilage condensation
true
true
Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints.
skeletal subdivision
subdivision of skeleton (in vivo)
subdivision of skeleton
true
Skeletal element that forms around the notochord and is part of the vertebral column.
vertebra skeletal element
vertebra element
vertebra endochondral element
vertebral endochondral element
vertebral element
true
The cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column.
vertebral cartilage condensation
vertebra cartilage element
true
true
The pre-cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column.
vertebral pre-cartilage condensation
vertebra pre-cartilage condensation
true
Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis.
solid joint
nonsynovial joint
true
Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.
axial skeletal system
true
Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints.
axial skeletal system
post-cranial axial skeletal system
postcranial axial skeletal system
true
A subdivision of an anatomical system.
organ system subdivision
true
Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints.
appendicular skeletal system
true
basal cell layer of skin
outer epithelium of body
embryonic skin basal layer
true
true
The collection of all skeletal elements in an individual limb or fin.
limb/fin skeleton
skeletal parts of limb/fin
skeleton of limb/fin
paired limb/fin skeleton
true
true
Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified].
stylopodium skeleton
mesomere 1
propodial skeleton
propodium
proximal metapterygial mesomere
stylopod
stylopodium
stylopodial skeleton
true
true
Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).
cell condensation
true
A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.
axial subdivision of organism
body segment
main body segment
subdivision of organism along main body axis
true
A cardiovascular system that is part of a conceptus.
conceptus cardiovascular system
embryonic circulatory system
fetal circulatory system
embryonic cardiovascular system
true
Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium.
irregular connective tissue
true
Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium.
irregular dense connective tissue
typus irregularis (textus connectivus collagenosus compactus)
dense irregular connective tissue
true
true
Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets
dense connective tissue
true
Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue.
textus connectivus collagenosus laxus
textus connectivus laxus
loose connective tissue
true
An acinus that is part of a exocrine gland.
exocrine gland acinus
acinus of exocrine gland
true
collection of collagen fibrils
true
A region of the stomach that is lined with glandular epithelium.
glandular stomach
stomach glandular region
true
blood that remains in the placenta and in the attached umbilical cord after childbirth[WP].
cord blood
fetal blood
umbilical cord blood
umbilical cord blood
true
A zone of skin that is part of a craniocervical region.
head or neck skin
true
An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]
columnar epithelium
true
Epithelium that derives from the mesoderm. [Automatically generated definition].
mesoderm-derived epithelium
mesoepithelium
meso-epithelium
true
true
internal anal region
true
Blood-forming tissue, consisting of reticular fibers and cells.
haemopoietic tissue
hematopoietic tissue
hemopoietic tissue
textus haemopoieticus
bone marrow tissue
hematopoietic tissue
true
true
The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle.
bones of lower limb
lower limb skeleton
ossa membri inferioris
pelvic complex skeleton
set of bones of lower limb
skeleton of posterior limb/fin and girdle
skeleton of pelvic complex
true
An epithelium that is part of a cloaca.
cloacal endoderm
cloacal epithelium
true
true
true
true
A section through the tube or network of tubes that connects the ovaries to the outside of the body.
subdivision of oviduct
subdivision of uterine tube
uterine tube zone
zone of uterine tube
subdivision of fallopian tube
subdivision of oviduct
true
true
subdivision of tube
true
An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].
foramen space
anatomical conduit space
true
A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
main body axis
true
The region of the organism associated with the visceral organs.
body
whole body
body proper
true
A organ component layer that is part of a integumental system.
layer of skin
skin layer
integumentary system layer
true
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
digestive organ
digestive system organ
digestive system element
true
Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.
skeleton of thorax
thoracic part of axial skeleton
thoracic skeleton
thoracic skeleton
true
A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory.
interlobular duct
true
A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles).
skeletal muscle
skeletal muscle organ
true
A portion of tissue that will develop into vasculature.
primordial vasculature
true
A hindlimb bone or its cartilage or pre-cartilage precursor.
hindlimb bone skeletal element
hindlimb endochondral element
true
A femur bone or its cartilage or pre-cartilage precursor.
femur skeletal element
femur element
femur endochondral element
true
A limb bone or its cartilage or pre-cartilage precursor.
limb bone skeletal element
limb bone endochondral element
limb endochondral element
true
true
Any structure that is placed on one side of the left-right axis of a bilaterian.
lateral structure
true
A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
heart
cardiac pump
heart or heart like organ
circulatory vessel
cardiac structure
circulatory organ
true
heart/pericardium
heart plus pericardium
true
portion of heterogeneous tissue
heterogeneous tissue
true
A epithelium that is part of a foregut.
foregut epithelium
true
Primordium that develops into the central nervous system
future CNS
presumptive central nervous system
future central nervous system
true
Primordium that develops into the nervous system
presumptive nervous system
future nervous system
true
The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.
extra-embryonic component
extraembryonic component
entire extraembryonic component
true
An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development.
transitional anatomical structure
true
A mesenchyme-derived anatomical entity undergoing a transtion to become another structure.
developing mesenchymal structure
true
skeletal musculature
true
lymphomyeloid tissue
true
An multicellular anatomical structure that has subparts of multiple organs as a part.
anatomical cluster
multi organ part structure
true
A cluster of cells, largely surrounded by a morphological boundary.
cell cluster
true
A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
anatomical collection
true
organ sector
organ zonal region
organ zone
organ region with floating fiat boundary
zone of organ
true
duct epithelium
ductal epithelium
epithelial layer of duct
true
excretory duct
true
An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.
cardiopharyngeal field
true
true
true
true
Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument.
external integument structure
true
length unit
A unit which is a standard measure of the distance between two points.
length unit
true
mass unit
A unit which is a standard measure of the amount of matter/energy of a physical object.
mass unit
true
time unit
A unit which is a standard measure of the dimension in which events occur in sequence.
time unit
true
temperature unit
A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
temperature unit
true
concentration unit
A unit which represents a standard measurement of how much of a given substance there is mixed with another substance.
concentration unit
true
volume unit
A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas.
volume unit
true
James Malone
Tomasz Adamusiak
ALS
ALS (Amyotrophic Lateral Sclerosis)
AMYOTROPHIC SCLEROSIS
Amyotrophic Lateral Sclerosis, Guam Form
Amyotrophic lateral sclerosis (disorder)
Dementia With Amyotrophic Lateral Sclerosis
Disease, Lou-Gehrigs
GEHRIGS DIS
Gehrig Disease
Gehrigs Disease
Guam Form of Amyotrophic Lateral Sclerosis
LOU GEHRIG DIS
LOU GEHRIGS DIS
Lateral Scleroses, Amyotrophic
Lou Gehrig Disease
Lou Gehrig's disease
MOTOR NEURON DIS AMYOTROPHIC LATERAL SCLEROSIS
Motor Neuron Disease, Amyotrophic Lateral Sclerosis
Motor neuron disease, bulbar
amyotrophic lateral sclerosis
DOID:332
GeneRIF:11675877
GeneRIF:11854284
GeneRIF:11854285
GeneRIF:11860274
GeneRIF:11943600
GeneRIF:11951178
GeneRIF:11991808
GeneRIF:11996514
GeneRIF:12039658
GeneRIF:12125045
GeneRIF:12127151
GeneRIF:12138710
GeneRIF:12153483
GeneRIF:12210393
GeneRIF:12217886
GeneRIF:12230304
GeneRIF:12235108
GeneRIF:12270696
GeneRIF:12393885
GeneRIF:12437574
GeneRIF:12441104
GeneRIF:12442272
GeneRIF:12446576
GeneRIF:12448348
GeneRIF:12458194
GeneRIF:12475980
GeneRIF:12480087
GeneRIF:12502789
GeneRIF:12528821
GeneRIF:12584731
GeneRIF:12614934
GeneRIF:12641746
GeneRIF:12644909
GeneRIF:12659845
GeneRIF:12677446
GeneRIF:12679596
GeneRIF:12694394
GeneRIF:12707786
GeneRIF:12730211
GeneRIF:12770687
GeneRIF:12783432
GeneRIF:12843244
GeneRIF:12847526
GeneRIF:12866199
GeneRIF:12870272
GeneRIF:12875980
GeneRIF:12915461
GeneRIF:12972170
GeneRIF:13129803
GeneRIF:13678668
GeneRIF:14506936
GeneRIF:14511332
GeneRIF:14596848
GeneRIF:14597108
GeneRIF:14642651
GeneRIF:14675609
GeneRIF:14676054
GeneRIF:14734542
GeneRIF:14970233
GeneRIF:14978393
GeneRIF:14985749
GeneRIF:14989597
GeneRIF:14991384
GeneRIF:15006704
GeneRIF:15019581
GeneRIF:15030390
GeneRIF:15033789
GeneRIF:15037546
GeneRIF:15048885
GeneRIF:15069187
GeneRIF:15076751
GeneRIF:15094483
GeneRIF:15106121
GeneRIF:15109247
GeneRIF:15126567
GeneRIF:15184633
GeneRIF:15233913
GeneRIF:15264227
GeneRIF:15313203
GeneRIF:15326253
GeneRIF:15330338
GeneRIF:15350647
GeneRIF:15388334
GeneRIF:15465081
GeneRIF:15475574
GeneRIF:15488469
GeneRIF:15509539
GeneRIF:15546588
GeneRIF:15557516
GeneRIF:15568021
GeneRIF:15623718
GeneRIF:15634772
GeneRIF:15652414
GeneRIF:15657392
GeneRIF:15657798
GeneRIF:15672551
GeneRIF:15691826
GeneRIF:15753080
GeneRIF:15776280
GeneRIF:15789135
GeneRIF:15829169
GeneRIF:15837590
GeneRIF:15910777
GeneRIF:15978558
GeneRIF:16005901
GeneRIF:16020530
GeneRIF:16114275
ICD9:335.20
MSH:D000690
NCIt:C34373
NIFSTD:birnlex_12566
SNOMEDCT:86044005
A degenerative disorder affecting upper MOTOR NEURONS in the brain and lower motor neurons in the brain stem and SPINAL CORD. Disease onset is usually after the age of 50 and the process is usually fatal within 3 to 6 years. Clinical manifestations include progressive weakness, atrophy, FASCICULATION, hyperreflexia, DYSARTHRIA, dysphagia, and eventual paralysis of respiratory function. Pathologic features include the replacement of motor neurons with fibrous ASTROCYTES and atrophy of anterior SPINAL NERVE ROOTS and corticospinal tracts (MeSH).
A degenerative disorder affecting upper MOTOR NEURONS in the brain and lower motor neurons in the brain stem and SPINAL CORD. Disease onset is usually after the age of 50 and the process is usually fatal within 3 to 6 years. Clinical manifestations include progressive weakness, atrophy, FASCICULATION, hyperreflexia, DYSARTHRIA, dysphagia, and eventual paralysis of respiratory function. Pathologic features include the replacement of motor neurons with fibrous ASTROCYTES and atrophy of anterior SPINAL NERVE ROOTS and corticospinal tracts. (From Adams et al., Principles of Neurology, 6th ed, pp1089-94)
An autosomal dominant inherited form of amyloidosis.
amyotrophic lateral sclerosis
URI: http://www.ebi.ac.uk/cellline#amyotrophic_lateral_sclerosis
true
true
James Malone
A disease is a disposition that describes states of disease associated with a particular sample and/or organism.
disease
true
tissue, organ, system, sperm, blood or body location (arm).
James Malone
Jie Zheng
Tomasz Adamusiak
MO_954
The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm).
organism part
URI: http://www.ebi.ac.uk/cellline#organism_part
true
James Malone
motor system
muscle
muscle system
muscles
musculature
musculature system
muscule system
AAO:0000307
BTO:0001485
EV:0100146
FBbt:00005069
MA:0000015
MAT:0000025
MFO:0002100
TADS:0000324
TAO:0000548
WBbt:0005737
ZFA:0000548
The bodily system that is composed of skeletal, smooth, and cardiac muscle tissue and functions in movement of the body or of materials through the body, maintenance of posture, and heat production.
muscular system
URI: http://www.ebi.ac.uk/cellline#muscular_system
true
James Malone
Tomasz Adamusiak
AAO:0000324
BTO:0001484
EHDAA:826
EMAPA:16469
EV:0100162
FBbt:00005093
FMAID:7157
MA:0000016
MAT:0000026
NIFSTD:birnlex_844
SAEL:71
TAO:0000396
WBbt:0005735
XAO:0000177
ZFA:0000396
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS).
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)
All the nerve centers and nerve fibers in the central, visceral and peripheral nervous systems.
The nervous system is essentially a biological information highway, and is responsible for controlling all the biological processes and movement in the body, and can also receive information and interpret it via electrical signals which are used in this nervous system. It consists of the Central Nervous System (CNS), essentially the processing area and the Peripheral Nervous System which detects and sends electrical impulses that are used in the nervous system.
nervous system
URI: http://www.ebi.ac.uk/cellline#nervous_system
true
James Malone
Tomasz Adamusiak
CNS
Cerebrospinal axis
Neuraxis
BTO:0000227
EHDAA:828
EMAPA:16470
EV:0100163
FMAID:55675
MA:0000167
MAT:0000457
NIFSTD:birnlex_1099
TAO:0000012
ZFA:0000012
Organ with organ cavity which consists of gray matter and white matter. Examples: There is only one neuraxis.
The brain and spinal cord.
The brain and spinal cord. Kimmel et al, 1995.
The central nervous system is that part of the nervous system that consists of the brain and spinal cord. The central nervous system (CNS) is one of the two major divisions of the nervous system. The other is the peripheral nervous system (PNS) which is outside the brain and spinal cord.
central nervous system
URI: http://www.ebi.ac.uk/cellline#central_nervous_system
true
Tomasz Adamusiak
muscular disease
DOID:423
myopathy
URI: http://www.ebi.ac.uk/cellline#muscular_disease
true
Bill Duncan <http://orcid.org/0000-0001-9625-1899>
2018-06-02T03:01:08Z
obsolete class
true
http://www.lincsproject.org/LINCS/centers/data-and-signature-generating-centers/lincs-pccse
The LINCS Proteomic Characterization Center for Signaling and Epigenetics at the Broad Institute
PCCSE
http://lincsproject.org/LINCS/centers/data-and-signature-generating-centers/lincs-transcriptomics
https://www.broadinstitute.org/
BROAD_T
example to be eventually removed
example to be eventually removed
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
metadata complete
organizational term
term created to ease viewing/sort terms for development purpose, and will not be included in a release
PERSON:Alan Ruttenberg
organizational term
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
ready for release
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
pending final vetting
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
group:OBI
to be replaced with external ontology term
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Alan Ruttenberg
group:OBI
requires discussion
right handed
right handed
ambidexterous
ambidexterous
left handed
left handed
Edingburgh handedness inventory
The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities.
PERSON:Alan Ruttenberg
PERSON:Jessica Turner
PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html
Edingburgh handedness inventory
axiom holds for all times
## Elucidation
This is used when the statement/axiom is assumed to hold true 'eternally'
## How to interpret (informal)
First the "atemporal" FOL is derived from the OWL using the standard
interpretation. This axiom is temporalized by embedding the axiom
within a for-all-times quantified sentence. The t argument is added to
all instantiation predicates and predicates that use this relation.
## Example
Class: nucleus
SubClassOf: part_of some cell
forall t :
forall n :
instance_of(n,Nucleus,t)
implies
exists c :
instance_of(c,Cell,t)
part_of(n,c,t)
## Notes
This interpretation is *not* the same as an at-all-times relation
axiom holds for all times
en
Ontology for Biomedical Investigations
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
Alan Ruttenberg
Allyson Lister
Barry Smith
Bill Bug
Bjoern Peters
Carlo Torniai
Chris Mungall
Chris Stoeckert
Chris Taylor
Christian Bolling
Cristian Cocos
Daniel Rubin
Daniel Schober
Dawn Field
Dirk Derom
Elisabetta Manduchi
Eric Deutsch
Frank Gibson
Gilberto Fragoso
Helen C. Causton
Helen Parkinson
Holger Stenzhorn
James A. Overton
James Malone
Jay Greenbaum
Jeffrey Grethe
Jennifer Fostel
Jessica Turner
Jie Zheng
Joe White
John Westbrook
Kevin Clancy
Larisa Soldatova
Lawrence Hunter
Liju Fan
Luisa Montecchi
Matthew Brush
Matthew Pocock
Melanie Courtot
Melissa Haendel
Mervi Heiskanen
Monnie McGee
Norman Morrison
Philip Lord
Philippe Rocca-Serra
Pierre Grenon
Richard Bruskiewich
Richard Scheuermann
Robert Stevens
Ryan R. Brinkman
Stefan Wiemann
Susanna-Assunta Sansone
Tanya Gray
Tina Hernandez-Boussard
Trish Whetzel
Yongqun He
2009-07-31
The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.
OWL-DL
An ontology for the annotation of biomedical and functional genomics experiments.
Ontology for Biomedical Investigation
http://creativecommons.org/licenses/by/4.0/
Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
2017-02-22
2018-05-23
See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo.
Caty Chung
Stephan Schurer
Asiyah Yu Lin
2018-01-26
Draft version
James Malone
Alexander Diehl
Jie Zheng
Yongqun "Oliver" He (YH)
Uma Vempati
Jiangan Xie
Hiroshi Masuya
Alex Ade
Daniel Cooper
The Cell Line Ontology.
Yue Liu
OWL-DL
Helen Parkinson
Sirarat Sarntivijai
An ontology for the domain of cell lines and cell line cells
2.1.135
CLO: Cell Line Ontology
Matthew Brush
Allen Xiang
Vision Release: 1.0.59
Yue Liu
Yongqun "Oliver" He (YH)
A biological ontology in the area of genes and genomes.
OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets.
OGG: Ontology of Genes and Genomes
12-01-2016
OWL-DL
Bin Zhao
This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's "meaningful use" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt
William Hogan
Mathias Brochhausen
Amanda Hicks
2017-06-08
Swetha Garimalla
The Ontology of Medically Related Social Entities
Daniel Welch
Shariq Tariq